- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] zone tool and volume rendering
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, I'll tell you my experience looking at a tomogram (2048 x 2048 x 76) of an immune synapse for a demonstration I gave last month at a cell tomography workshop. The file (mrc) is too large to conveninently display at full resolution. So I made binned versions 2x and 4x smaller along each axis (file size 8x or 64x smaller). Then I used the precomputed subsamples feature I described before. For some added convenience I then saved the map to a NetCDF file using Chimera because this saves the full matrix and binned versions in a single file (new in Chimera 1.2318). I use the volume dialog data display options to "Adjust step size to show at most 1 Mvoxels", or however many million voxels my computer can handle without getting too slow. Then I use the full view of the data to find regions I'm interested in, then use the subregion selection feature and Crop button to look at a smaller piece and the step size automatically is reduced. If I choose a small region I get full resolution. When doing this you have to keep in mind that once you manually change the step size at the top of the volume dialog it turns off the automatic step size adjustment. So I try to avoid that. Of course I also use the volume planes tool. I think you know all this and probably are using Chimera to the best of its current capabilities. You want to push it to use better compression (like resampling to have better aligned boxes) so you can see more data at full resolution. We don't have that yet. It is not hard to envision much fancier compression implementations that improve performance. Chandra Bajaj at U. Texas is very interested in this and may have software you can use. You might want to try his VolumeRover program. The Chimera EM capabilities were developed for single particle reconstructions. We have done little in Chimera to support work with EM tomograms which are very different in size and content (non-axis aligned structures, membranes, ...). We plan to develop tomogram capabilities and my volume planes tool created last month is a tiny step. But it will take years to implement the obvious stuff we can think of now. Your comments are helpful in guiding the priorities. I don't understand why you are "jotting down displacements" when saving subregions. Chimera puts that info into the MRC header. So why do you need to write it down? Tom Jeff wrote: > thanks Tom, > > with regards to the rotation/resampling, I was thinking mainly in > terms of visualizing large #'s of filaments and membrane, which in > themselves only constitute a small fraction of the actual volume they > traverse. even if re-sampling were done by cubic interpolation onto a > the same dimensioned grid, in some cases the loss in resolution would > be acceptable (definitely would be acceptable for some of my current > needs). i have problems with visualizing my whole maps unbinned but > was thinking that the savings such an approach would represent could > allow me to do that. for instance, this is already a problem for me > with trying to volume render a slab of membrane, which I think might > contain interesting features but I can't get the whole thing to go > unbinned; if it were rotated into the minimal enclosing volume, > interpolation artifacts or otherwise, my feeling was that I might > overcome that (there are also a bunch of filaments attached to the > membrane, and running underneath the membrane, so it is a real > difficulty for me to go back and forth between cutting out subvolumes > and binning them to be manageable, segment out filaments, or membrane, > etc, then try to put all the segmented items back into the same volume > and have a look-see). > > the volume planes tool has proven very helpful in segmenting out the > membranes, though. to get at the filaments that are attached to the > membrane, I was zoning out a region around the membrane (placed a > bunch of markers on the membrane using volume planes tool) about 400 A > in radius, but this proved difficult to render in the entire tomogram > b/c the zoned membrane still encompassed most of the original volume, > etc. so I was back to having to cut regions out of that segmented > membrane map to look further. (thus necessitating me jotting down the > displacements of each subregion, etc.) > > -jeff

1 0

Re: [Chimera-users] using a marker file to zone a volume from python prompt
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, I forgot to mention that to run the volumezone.py script without display the Chimera user interface you would invoke it from a shell: % chimera --nogui volumezone.py The --nogui flag tells Chimera not to start any graphical user interface. Tom

1 0

Re: [Chimera-users] zone tool and volume rendering
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, You are right that masking a filament that runs along the long diagonal of a box does not reduce the disk space or memory use any. (If you compressed the file then it would make a big difference. But you need to uncompress it to use it so that is of limited value.) So to achieve a space savings you need to resample the volume using a grid aligned with the axes of the filament. The resampling will degrade the data resolution some and it might be reasonable to do it on a grid with half the spacing (making the file 8x bigger). With such a resampled map the rotation and shift could be stored so that it can be placed in the original location in the full map. We don't support that now but when we add resampling we will store those rotation parameters in the map file header (maybe in the "labels" field for an MRC file). The time for Chimera to display a map depends on how large the volume grid is because it scans the entire grid in one pass when using the marching cubes algorithm to compute a contour surface. It also depends on how many triangles make up the contour surface. By eliminating the 99% of a masked file that is zeros using a new orientation and resampling it could compute contour surfaces faster. And the solid (volumetric) rendering should be faster directly proportional to the file size. That may be the more important case for your EM tomograms. I plan on supporting resampling on a rotated grid. But I think in many real uses it will not save much space because you will want to resample with finer grid spacing. But it could be convenient for exporting to analysis or visualization software that is limited to xy-planes. Tom Jeff wrote: > got it, > > what you say makes sense, I can definitely workaround, especially given > that the zone tool does a mask upon saving. > > I have been thinking about the problem I have with filaments (or > surfaces) spanning non-orthogonal regions of a volume, which means that > zoning out a long filament (or surface) that might take a much smaller > amount of space/memory once zoned actually takes up almost the same > amount currently, if I am thinking right. > > as an example, say you have a volume that is 100x100x100. inside the > volume, you have a filament, that takes up 10x10x244 voxels (effectively > spanning from one corner to the mirror/opposite corner of the volume). > in theory, zoning out that filament could take up ~1/40th the space, if > rotated to line up with one of the cartesian axes. I don't know how much > logic it would take to do this; I also don't know how chimera reads > origin information from an MRC file, or how much work it would take to > enable it to read (and use) an euler convention from an MRC file, for > displaying later. This would enable cutting a whole bunch of filaments > out of a volume, and then displaying them all concurrently without > running into the problem of loading in large rectangular prisms of space > that are mainly zeros (if this is currently happening, I don't know). I > guess at that point it makes sense to consider the geometric center of > such a rotated object at its origin, to reduce re-displaying the > object/filament properly in the original orientation to just storing a > shift and the rotation angles (6 parameters). > > the same holds true for membranes - right now, I have an entire membrane > that I segmented with markers, but it essentially runs along a hypotenuse. > > one question that probably negates the above paragraph would be 'does > the masked volume (with mostly zeros) display any faster / take less > resources than an equivalent volume without the zeros'? I have been > assuming this is not the case, that the zoned/masked volume still > entails reading in / accounting for that full rectangular prism, despite > the fact that it is mostly empty / full of zeros. > > thanks for you help, > > -Jeff

1 0

Re: [Chimera-users] using a marker file to zone a volume from python prompt
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, I've attached a script that opens a density map and a Chimera marker file and writes a new volume corresponding to a zone around the markers. It does not require showing the Chimera user interface to do this. Perhaps you don't need this now (I just got your follow-up email.) but perhaps you will find it useful in writing other scripts. Karin Gross at Max Planck Institute of Biochemistry has written a Chimera extension to slice tomograms at arbitrary angles. I saw it when I visited Munich in December. They also were planning on allowing marker placement on those planes. The volume planes tool could be made to average neighboring planes. Currently it simply displays a NxMx1 subvolume in solid rendering mode. Since there is no existing code in Chimera to support averaging adjacent planes that would have to be added. Probably the easiest solution is to add the adjacent planes in Python and create a new single plane volume on the fly. Tom Jeff wrote: > thanks Tom, > > I will try that. alongside that, is there a way for me to run a 'zone' > function and save a subregion from a python command line (no chimera > launched, just import a library?)? > > I have used the volume planes tool to generate a marker set of a > membrane, it was handy. But, it only handles orthogonal directions, it > can't provide an arbitrary interpolant (which is a large reason I rely > heavily on IMOD's slicer tool); this functionality would be very useful. > A second addition to the volume planes tool would simply be allowing > averaging several slices together (reduces noise) in the direction > normal to the planes, which may already be there (the documentation > online said something about this feature, but it wasn't clear to me) > > it the volume planes tool were able to handle an arbitrary > view/interpolant, then I wouldn't have to depend on the slicer tool, and > the previous request about rotating markers that was related to that > requirement (different features available in different slicer > orientations in IMOD, necessitating a rotation prior to visualization > with the volume planes tool in chimera, thus requiring old marker set > from original volume to be rotated to be used in new volume, etc) would > effectively be voided > > > -Jeff # ---------------------------------------------------------------------------- # Save a volume zone around a given set of markers as a new volume file. # def save_zone(volume_path, markers_path, radius, volume_out_path): # Read zone points atoms, bonds = marker_set_atoms_and_bonds(markers_path) from chimera import Xform xform = Xform() # Identity transform for marker points from SurfaceZone import path_points points = path_points(atoms, bonds, xform) from VolumeData import open_file_type vol = open_file_type(volume_path, 'mrc') # Get containing volume subregion ijk_min, ijk_max = containing_subregion(vol, points, radius) from VolumeData import Grid_Subregion subvol = Grid_Subregion(vol, ijk_min, ijk_max) # Make new volume with zeros outside radius from VolumeViewer import zone_masked_grid_data masked_vol = zone_masked_grid_data(subvol, points, radius) # Write new volume from VolumeData.mrc import write_mrc2000_grid_data write_mrc2000_grid_data(masked_vol, volume_out_path) # ---------------------------------------------------------------------------- # def marker_set_atoms_and_bonds(markers_path): from VolumePath.markerset import load_marker_set_xml msets = load_marker_set_xml(markers_path) atoms = [] bonds = [] for mset in msets: atoms.extend(map(lambda m: m.atom, mset.markers())) bonds.extend(map(lambda l: l.bond, mset.links())) return atoms, bonds # ---------------------------------------------------------------------------- # def containing_subregion(vol, points, radius): from VolumeViewer import points_ijk_bounds, clamp_region ijk_min, ijk_max = points_ijk_bounds(points, radius, vol) ijk_min, ijk_max = clamp_region((ijk_min, ijk_max, None), vol.size)[:2] from math import floor, ceil ijk_min = map(lambda x: int(floor(x)), ijk_min) ijk_max = map(lambda x: int(ceil(x)), ijk_max) return ijk_min, ijk_max # ---------------------------------------------------------------------------- # volume_path = '/usr/local/src/chimera-demos/volume/examples/tricorn_map.mrc' markers_path = '/usr/local/src/staff/goddard/chimera/devel/ZoneScript/test.cmm' radius = 5 volume_out_path = '/usr/local/src/staff/goddard/chimera/devel/ZoneScript/test.mrc' save_zone(volume_path, markers_path, radius, volume_out_path)

1 0

access to pdb parser
by Jean Didier Pie Marechal 29 Jan '07

29 Jan '07

2 1

Re: [Chimera-users] zone tool and volume rendering
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, The volume dialog "zone" feature does not work with solid (volumetric) rendering. The current implementation just hides surface triangles having vertices outside the given range so it only works on surfaces. When you use volume dialog File / Save map as... it makes a copy of the data with grid values set to zero outside the radius. Creating a copy of the map in memory or masking the map for use with solid rendering are not currently supported. We wish to add this in the future and it should not be hard to achieve although performance when changing the radius will be significantly worse than with the current surface zoning. The documentation does not mention this limitation and I will update the volume dialog description to describe it. Tom Jeff wrote: > hi Tom, > > is there a way to get the zone tool to operate when doing a solid/volume > rendering - in surface mode, if you set a zone radius, let's say 40 A, > you'll get a region that extends 40 A around the selected marker(s); > however, in 'solid' mode, it appears I get the entire orthogonal region > in the volume that encloses the markers plus that radius. thiis is > problematic if the markers span the hypotenuse of the volume; in that > case, zone with volume/'solid' appears to more or less display the > entire volume rather than just the surrounding region as in 'surface mode' > > do I have a buggy version? this is a recent release, but I've had this > happen with previous releases > > -jeff

1 0

Re: [Chimera-users] chimera startup problem
by Greg Couch 29 Jan '07

29 Jan '07

Just a FYI to the list, the problem here was an ancient OpenGL graphics driver. Upgrading it made the problem disappear. I'll be adding an entry to our Graphics Driver bugs web page, <http://www.cgl.ucsf.edu/chimera/graphicsbugs.html> with a few more details. - Greg ---------- Forwarded message ---------- Date: Tue, 23 Jan 2007 12:25:41 -0500 From: Chen Xu <xuchen66(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] chimera startup problem Dear List, after upgrading to 1.2304 (1.2303 freeze the computer after several minute loaded with a volume pdb file) , I have problem to start it up on (RedHat): agnieszka@raptor ~]$ chimera Error starting chimera: ValueError: attempt to create string with null pointer (see reply log for Python traceback info) Traceback (most recent call last): File "/sware/chimera/chimera-1.2304/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 255, in init tkgui.initializeGUI(exitonquit) File "CHIMERA/share/chimera/tkgui.py", line 2407, in initializeGUI File "CHIMERA/share/chimera/tkgui.py", line 2368, in createApp File "CHIMERA/share/chimera/tkgui.py", line 1784, in __init__ File "CHIMERA/share/chimera/tkgui.py", line 1811, in makeGraphicsWindow ValueError: attempt to create string with null pointer any help?

1 0

Slow rendering in FC6
by Thomas Goddard 29 Jan '07

29 Jan '07

On Yifan's linux system a large molecule takes a second to redraw and gradually renders from one side to the other. Turned out he did not have the NVIDIA graphics driver installed, so MESA software rendering was being used. Determined this using linux "glxinfo" command. Solution was to install graphics driver. -------- Original Message -------- Subject: problem of running Chimera in FC6 Date: Sun, 28 Jan 2007 13:05:20 -0800 From: Yifan Cheng To: goddard(a)cgl.ucsf.edu Hi Tom, I have a question about running Chimera in Linux FC6 system and wondering if you could help me out? I have Linux boxes running FC6, with a Gigabyte GV-NX76G256D-RH Geforce 7600GS 256MB video card. But somehow the Chimera keep refreshing with any movement in the model or map I loaded into it. It runs this way in both thousands color mode as well as in millions color mode. This video card is not Quadro type and has no stereo function, but I thought this shouldn't matter. Do you have any idea what might be the problem? Thanks a lot for your help. best, Yifan

1 0

Re: [Chimera-users] align different scale models
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Pu, The PDB file uses units of Angstroms. To specify the spacing between grid planes of your EM map, open it in Chimera, then use menu entry Features / Origin and Scale from the volume dialog. The "voxel size" values listed indicate the size of one grid cell in the density map which is equivalent to the grid spacing. You can change the values and press Return (or Enter) key and the map will be shown at the new scale. Enter the values in Angstroms. (Chimera does not know what units you are using but all data sets must use the same units if you want them to be displayed at the correct relative scales.) The map file is not modified. To save the new scale you either can save a Chimera session (File / Save session as... on the main Chimera window) or save a new copy of the map (File / Save map as... on the volume dialog). Tom P Qian wrote: > Hi Tom, > > I have question to ask you about alignment of PDB model and EM density map. > > When I open both EM density map and its corresponding PDB model, I found they > have different size. I think that is due to different scale they are using. My > question is: Is it possible for me to re-scale them individually so that they > can match each other. I cannot do it at the momemt because zoom function will > affect all data loaded, not only active data but also unactive one. I'm trying > to produce a EM density map which has same scale with PDB model to solve it, > but if Chimera could do it as well, it will be helpful. Thanks > > Best regards > > P. Qian > > Dr. Pu Qian > Physics Department > The University of Sheffield > Hicks Building > Hounsfield Road, S3 7RH > UK >

1 0

Re: [Chimera-users] using a marker file to zone a volume from python prompt
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, I understand your problem. I think you can handle the large data sets interactively using the "precomputed subsample" feature of the volume dialog. As you mentioned you need to create smaller binned versions of your data. Then you open your full size map in Chimera but do not display it. Then you use Features / Precomputed Subsamples and add the binned file (ie. subsampled data). Then when you display the data with step sizes larger than 1 where it can use the binned data it will use the binned data. In this way Chimera never needs to open the full data if you only display at binned step sizes. You can then use the zone or subregion box tools to specify a smaller piece of the map and then use the volume dialog "File / Save map as" menu entry. That always says at full resolution, so the needed part of the full size map will be read when you do that. There is a Chimera script for creating the binned data (chimera/share/VolumeProcessing/downsize.py) described in the Volume Viewer documentation in the Chimera User's Guide: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… Another useful tool for handling tomograms that are too large to display in Chimera at full resolution is the Volume Planes module that can be downloaded from the Chimera experimental features page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html When you display just one plane at a time, Chimera only loads that plane from the map file (for most map file formats, e.g. MRC). This can allow you to flip through the planes at full resolution while having just a limited amount of data in memory at any one time. Tom ---- Date: Jan 29, 2007 hi Tom, is it possible for me to use a (previously generated) chimera marker file to zone and save a region from a volume map from a python prompt, without launching chimera? A lot of volumes I use are simply too big to handle in chimera, and if I chop up large volumes, I might have filaments running across the borders that I cut, etc. When I have done such 'chopping out' of subvolumes, it is often difficult for me to figure out which filaments I care about (or where they are ...) a priori. One solution I was thinking of is to use a several-times binned file to generate a marker file using chimera, and then to use the zone tool from a python prompt on the unbinned volume, without having to launch chimera and try to actually visualize the full, unsegmented volume. can I do this? (or, does this question make sense?) thanks, -Jeff

1 0

Color using Beta factor
by Batsal Devkota 24 Jan '07

24 Jan '07

Hi, Is it possible to color the atoms according to their beta factor? Also, is there anyway I can search "the chimera-user archives"? batsal. -------------------------------------------------- Batsal Devkota Graduate Student, School of Biology GeorgiaInstitute ofTechnology Atlanta, GA 30332-0400

2 1

Re: [Chimera-users] defining rotation of a chimera markers file
by Thomas Goddard 24 Jan '07

24 Jan '07

Hi Jeff, Attached is a Python script to rotate Chimera markers about the origin using specified Euler angles. You open the script with Chimera menu entry File/Open... to apply the rotation which is specified at the end of the script. Tom Jeff wrote on Wed, Jan 24, 2007: thanks Tom (and Elaine), did not have the chance to reply yet. I have not done a whole lot w/ Euler angles in general but do know there are several conventions - seems like one for each package... As for a convention, the reason this came up is b/c the slicer tool in the IMOD viewer allows the user to rotate the volume according to the angles listed in the slider tool window. I use IMOD quite a bit to look plane by plane in various orientations in a reconstruction, and I'd like to be able to go back and forth with chimera (the IMOD extension in chimera only cycles through z; for an arbitrary plane, one would have to rotate the volume and reload into chimera). So, the convention used by IMOD would be preferred by me, for practical reasons. Here's the manpage for 'rotatevol' in IMOD, which mentions the convention: http://bio3d.colorado.edu/imod/doc/man/rotatevol.html 15 lines of code is fine; I might actually be able to dissect something that size and use it to learn. If I had a script I could do it through a python prompt, which would get me started. A command in chimera would be nicer, but not required (same goes for a graphical interface). You know, if I knew how to import the marker positions into an array in python, I could probably play with this myself - I guess I would also have to know how to write out the file too, and I'd have to brush up on my rotations. I have scanned through the contents of a marker file (`cat foo.cmm | less`, for example) and realize it is text, but I don't have enough familiarity with python to parse it into something useful. If you were to write a simple script, for basic I/O of a marker file (or tell me how to go about that) and a rotation matrix / execution as an example, I could probably run with that. For instance, if I do some things in EMAN or SPIDER, I might be able to adjust the convention when needed without further assistance. At some point, I'd like to know enough to make extensions for chimera, but lack the time to plug away at it. -Jeff # ------------------------------------------------------------------------------ # Rotate all markers in the active path tracer marker set. # def rotate_markers(xform): from VolumePath import volume_path_dialog d = volume_path_dialog() if d == None: return # No marker sets exist. ms = d.active_marker_set if ms == None: return # No marker set chosen in dialog. from chimera import Point for m in ms.markers(): xyz = m.xyz() # Python tuple txyz = xform.apply(Point(*xyz)).data() m.set_xyz(txyz) # ------------------------------------------------------------------------------ # Convert Euler angles to an equivalent Chimera transformation matrix. # # Angles must be in degrees, not radians. # # Uses the most common Euler angle convention (the chi-convention) described at # # http://mathworld.wolfram.com/EulerAngles.html # def euler_transform(phi, theta, psi): from chimera import Xform, Vector xf1 = Xform.rotation(Vector(0,0,1), phi) # Rotate about z-axis xp = xf1.apply(Vector(1,0,0)) # New x-axis xf2 = Xform.rotation(xp, theta) # Rotate about new x-axis zp = xf2.apply(Vector(0,0,1)) # New z-axis xf3 = Xform.rotation(zp, psi) # Rotate about new z-axis xf = Xform() xf.premultiply(xf1) xf.premultiply(xf2) xf.premultiply(xf3) return xf # ------------------------------------------------------------------------------ # xf = euler_transform(30, 60, 45) rotate_markers(xf)

1 0

Problem loading trajectories ....
by sharada 23 Jan '07

23 Jan '07

Dear Chimera-users, Hello, I am a brand new entry into this forum. I have started using chimera recently. I use Gromacs for my molecular modeling work. Till I become friendly with chimera I need your valuable suggestions and cooperations. I request you to kindly bear with my very silly doubts and questions. Let me explain my problem. I have a protein of 35 residues and have simulated in a box of water for 10ns. My protein has charge so in order to neutralize it I have added counterions randomly placed them in the solvent(water). The counter ions that I am adding are Cl- ions. I have created a *.trr file of the tracjectory for this 10ns. I would like to visulaize this trajectory using chimera. I am using Tools /MD/Ensemble Analysis /MD Movie to load the trr file. when I do so I am getting the following error: Unknown molecule type: CL- TypeError: __len__() should return an int (see reply log for Python traceback info) Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 318, in init tkgui.eventLoop() File "CHIMERA/share/chimera/tkgui.py", line 2675, in eventLoop File "CHIMERA/lib/python2.4/lib-tk/Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1751, in __call__ File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1814, in _reporterror File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1377, in displayerror File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ File "CHIMERA/share/chimera/baseDialog.py", line 231, in <lambda> File "CHIMERA/share/chimera/baseDialog.py", line 473, in OK File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 87, in Apply File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 30, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 218, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 229, in _readHeader File "CHIMERA/lib/python2.4/xdrlib.py", line 194, in unpack_fstring if j > len(self.__buf): TypeError: __len__() should return an int What exactly is the problem ? How to solve it ?

4 3

File open
by Bill altenberger 23 Jan '07

23 Jan '07

We are considering using the program in a general lab environment. However, when we do a file open we are able to browse the contents of our C drive even though we have it restricted with windows group policies. Is there a way to force the program to open to a specific location and not over ride windows group policies? Thanks.

2 1

chimera startup problem
by Chen Xu 23 Jan '07

23 Jan '07

Dear List, after upgrading to 1.2304 (1.2303 freeze the computer after several minute loaded with a volume pdb file) , I have problem to start it up on (RedHat): agnieszka@raptor ~]$ chimera Error starting chimera: ValueError: attempt to create string with null pointer (see reply log for Python traceback info) Traceback (most recent call last): File "/sware/chimera/chimera-1.2304/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 255, in init tkgui.initializeGUI(exitonquit) File "CHIMERA/share/chimera/tkgui.py", line 2407, in initializeGUI File "CHIMERA/share/chimera/tkgui.py", line 2368, in createApp File "CHIMERA/share/chimera/tkgui.py", line 1784, in __init__ File "CHIMERA/share/chimera/tkgui.py", line 1811, in makeGraphicsWindow ValueError: attempt to create string with null pointer any help? -- Chen Xu Brandeis University Rosenstiel Center, MS029 Waltham, MA 02454 phone: +1 781 736 2469 fax: +1 781 736 2419

1 0

defining rotation of a chimera markers file
by Jeff 22 Jan '07

22 Jan '07

hello, is there a way to rotate a chimera markers file in a defined way, for instance by providing a sequence of euler angles? The context is in the case of defining a marker set in a a particular volume map, say volume A, and then doing additional processing of volume A outside of chimera, perhaps just a simple series of rotations, creating volume B. now, I would like to use the same marker set in a precise way on volume B (without just visually rotating it into place by hand). is there a way to apply the same rotations to the marker set? thanks, -Jeff

2 1

Experimental features
by Edmond Alexander 22 Jan '07

22 Jan '07

Good Morning, I have attempted to load some of the Chimera "Experimental Features" following the installation instructions: > On Macintosh computers put it in > > Chimera.app/Contents/Resources/share > > > On the Mac you will need to use Finder menu entry Go / Go to Folder... > to see inside the Chimera.app folder. > > When Chimera.app/Contents/Resources/share is typed into the Go To Folder I get a message that the "Folder can not be found". Subsequent searches show only the Chimera application. I am running a Mac G4 running Mac OS 10.3.9 and iMac (Mac Intel) running Mac OS 10.4.8 My Chimera version is 1.2303 Am I missing something? Your help will be greatly appreciated. Thanks in Advance, Edmond Alexander Alexander & Turner Medical Illustration Studio

2 2

hbonds and addh geometry
by Jim Procter 22 Jan '07

22 Jan '07

Hi all. Has anyone noticed and/or fixed the slight problem with applying the hbonds command (without 'sloppy' bond geometry allowed) after adding hydrogens to a structure with addh ? The identified hbonds are marked between donor and acceptor, but the donor's proton seems often seems to lie some way off the hbond vector by a seemingly consistent amount, suggesting a systematic error in the addh protonation geometry. As an aside to this, it would be very nice to be able to re-connect the detected hydrogen bonds so that the bond vector lies between the proton and the acceptor, rather than between the heavy atoms. Does anyone have a script to do this ? thanks in advance! Jim Procter -- ------------------------------------------------------------------- J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk

2 1

Using 3dconnexion 6DOF controller with Chimera
by Shi Jiye (ROC) 22 Jan '07

22 Jan '07

Hello, Does Chimera support 6DOF controllers such as SpaceExplorer from 3dconnexion? It would be nice to have this feature. Thanks, Jiye Shi **************************************************************************** Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail.

2 1

AA and DNA base-pair substitutions
by David Segal 22 Jan '07

22 Jan '07

Dear Chimera-users, I would often like to take a pdb of a protein-DNA complex and just change one aa or one base pair. Can Chimera do this? If not, does anyone know of free software that can (for example, Swiss-PDB Viewer can mutate an aa, but not a base). Thanks in advance. - Dave Segal -------- David J. Segal, Ph.D. University of California, Davis Genome Center/Pharmacology 4513 GBSF 451 E. Health Sciences Dr. Davis, CA 95616 Tel: 530-754-9134 Fax: 530-754-9658 Email: djsegal(a)ucdavis.edu Web: www.genomecenter.ucdavis.edu/segal/ NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message

2 1

save mol2 command
by Huang, Shengyou 22 Jan '07

22 Jan '07

Hi, Does anybody know a COMMAND which can save a mol2 format file in Chimera? Thanks! Shengyou Huang

3 3

yet another chimera question...
by Jeff 19 Jan '07

19 Jan '07

good morning Tom, there isn't by chance a way to output the orientation/location of a given model (or, likewise, its corresponding per-model clipping plane) so that I can write down particular views that are useful, without having to re-save chimera sessions with unique IDs (my kludge as of right now). and a related follow-up - if so, how do I re-input the orientations by command line in chimera (if possible?) thanks, -jeff

4 6

clarification regarding the application of chimera...
by harini senthil 19 Jan '07

19 Jan '07

I am a final year b.tech industrial biotech student working on docking studies between a polymer and membrane proteins of e.coli. I would like to know whether chimera can be utilised for performing polymer protein docking studies. Thanking you --------------------------------- Heres a new way to find what you're looking for - Yahoo! Answers

2 1

Re: [Chimera-users] chimera to rebuild crystal
by Elaine Meng 18 Jan '07

18 Jan '07

Maybe a more integrated solution would be to put the additional option(s) in Unit Cell - easy for me to say, however! 8-) Elaine On Jan 12, 2007, at 2:15 PM, Thomas Goddard wrote: > Hi Elaine, > > Brady Bernard wanted to output multiple unit cells, more than 3x3x3 > in > fact (which is what multiscale can do). The script lets you set the > number > of unit cells along each axis. That isn't supported in Unit Cell. > > Sorry the Brady email wasn't posted to chimera-users. Nag Eric about > that since the original email went directly to him. Of course, I too > now > have personal email messages from Brady that should have gone to > chimera-users. > I am still figuring out how to forward the mail and have the original > sender's name appear in the chimera-users archive summary. > > Tom

4 6

Re: [Chimera-users] Export idatmType
by Eric Pettersen 18 Jan '07

18 Jan '07

On Jan 17, 2007, at 10:47 PM, Brady Bernard wrote: > is there a way to do this with --nogui so that i can automate it in > a script? > > thanks, > brady It's pretty easy to make a Python script that opens a file, loops through open molecules and then their atoms, and prints our the atom identifier and IDATM type to that file. Here's an example: import chimera f = open("types.txt", "w") for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print>>f, a, a.idatmType f.close() If you save the above into a file with a ".py" suffix (e.g. types.py), then you could save all the types of 1gcn with "chimera -- nogui pdb:1gcn types.py", which would create a file named "types.txt" (in the same folder as types.py) with the types listed. BTW, you need to preserve the indentation of the Python code above -- it matters to Python. If you're automating this in a shell script, it may be simpler to just print the info to standard output and redirect that into a file, rather than open the file in the Python script. The command would then be "chimera --nogui --nostatus pdb:1gcn types.py > 1gcn_types.txt" (note the "--nostatus" flag so that status messages don't get mixed into the output). The Python script becomes: import chimera for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print a, a.idatmType --Eric > ----- Original Message ----- > From: Eric Pettersen > To: Brady Bernard > Cc: Thomas Goddard ; Elaine Meng > Sent: Tuesday, January 16, 2007 4:40 PM > Subject: Re: Export idatmType > > Hi Brady, > Tom forwarded your mail to me. There almost is a way. In the > 1.2318 snapshot, the Render By Attribute tool allows you to save > attribute values to a file using that tool's "File->Save > Attributes..." menu item (saved in the format that Define Attribute > accepts). So, why "almost"? The idatmType attribute is screened > out of the list of available attributes since it can be expensive > to compute the values -- and since you could already select by > IDATM type using the regular selection menu. But now that save > exists I will have to improve Render By Attribute so that it can > know that idatmType values are strings ahead of time (so it doesn't > have to ask for any values to figure that out). > Anyway, for your purposes it is not too hard to force Render By > Attribute to show you idatmType. First, get the 1.2318 release. > Then edit the file <your Chimera>/share/ShowAttr/__init__.py (on a > Mac: Chimera.app/Contents/Resources/share/ShowAttr/__init__.py) > and edit line 24. It will look like this: > > 'name': False, 'idatmType': False, 'idatmIsExplicit': False, > > change it to: > > 'name': False, 'idatmIsExplicit': False, > > Save the file and thereafter Render By Attribute should show you > the idatmType attribute. > > --Eric > >> hi tom - is there a quick way to save the atom types from >> idatmType to a text/log file along with the atom name or number? > >

1 0

Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 18 Jan '07

18 Jan '07

Now it works perfectly! Thanks Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 5:04 PM To: Zoghbi, Maria Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Movie resolution Hi Maria, Sorry the code I suggested was not correct. The new lines should have images = ... instead of image = ... Otherwise your change looks correct. Tom

1 0

For Chimera mac users
by Eduardo Sanz-Garcia 17 Jan '07

17 Jan '07

3 2

Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

I made the change (please, see document attached to be sure I did it right). When I restarted Chimera and tried to record a movie there was an error message (see reply log attached). Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 4:16 PM To: Zoghbi, Maria Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Movie resolution Hi Maria, Ok, so the bug is not fixed in Chimera version 1.2304. I made a note of that in our bug database. Here is a suggestion from the original bug report that solved the problem in that case: Edit the file in you Chimera 1.2304 distribution chimera/share/MovieRecorder/RecorderHandler.py using any text editor to change line 97 from image = chimera.viewer.pilImages() to width, height = chimera.viewer.windowSize image = chimera.viewer.pilImages(width, height, supersample = 1, opacity = False) Make sure to use the same indentation as the original code since this is important in the Python language. Then restart Chimera and try movie recorder again. Let me know if that fixes the problem. Tom

2 1

Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

I see. Thanks. I am using the version 1.2304, and the platform is Windows XP. Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 1:45 PM To: Zoghbi, Maria Subject: Re: [Chimera-users] Movie resolution Hi Maria, This is a bug. The movie capture should work for any window size without artifacts. This Chimera bug was reported earlier: http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=3151&database=ch imera Pressing the "view audit trail" button on that bug report page gives more info -- more than you want to konw. Supposedly that bug was fixed in Chimera version 1.2297. If you are using a newer version of Chimera than that and you still have this problem, then send me email with your Chimera version number and platform (Windows, Linux, Mac). Tom

2 1

bond rotation buglet
by Eric Pettersen 17 Jan '07

17 Jan '07

I just found out that the current release has a bug where it sometimes claims that a bond is terminal (and therefore won't let you rotate it) when it isn't. This occurs when there is already an active bond rotation adjacent to the desired new rotation, and the atom in common would have all its bonds in rotations. You can work around the problem by deactivating the other rotation (in the panel showing the rotations, click on the label for the rotation (under "Bond") which brings up a menu of actions, one of which is Deactivate). I also have a code fix that I could send to people that need it -- just drop me an email. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

Hello, I'm trying to make a movie, but the only format that I have been able to make work is the VCD (Video Compact Disc), which produces a low resolution movie (457x240). As soon as I change to a different standard format the recorded images are totally wrong (rotated, shifted, wear lines, etc). I have tried to choose my own resolution and the only one that has worked is when high=3/2width, but only when high ≤ 300. Are these restrictions for the resolution of the movies normal or am I doing something wrong? How can a make a higher resolution movie? I appreciate any help. Thanks Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu

2 1

Re: [Chimera-users] Export idatmType
by Eric Pettersen 16 Jan '07

16 Jan '07

Hi Brady, Tom forwarded your mail to me. There almost is a way. In the 1.2318 snapshot, the Render By Attribute tool allows you to save attribute values to a file using that tool's "File->Save Attributes..." menu item (saved in the format that Define Attribute accepts). So, why "almost"? The idatmType attribute is screened out of the list of available attributes since it can be expensive to compute the values -- and since you could already select by IDATM type using the regular selection menu. But now that save exists I will have to improve Render By Attribute so that it can know that idatmType values are strings ahead of time (so it doesn't have to ask for any values to figure that out). Anyway, for your purposes it is not too hard to force Render By Attribute to show you idatmType. First, get the 1.2318 release. Then edit the file <your Chimera>/share/ShowAttr/__init__.py (on a Mac: Chimera.app/Contents/Resources/share/ShowAttr/__init__.py) and edit line 24. It will look like this: 'name': False, 'idatmType': False, 'idatmIsExplicit': False, change it to: 'name': False, 'idatmIsExplicit': False, Save the file and thereafter Render By Attribute should show you the idatmType attribute. --Eric > hi tom - is there a quick way to save the atom types from idatmType > to a text/log file along with the atom name or number?

1 0

Fwd: chimera to rebuild crystal
by Eric Pettersen 16 Jan '07

16 Jan '07

Hi Tom, Brady's question below seems more up your alley somehow. It also seems like one of those things that should be cross-posted to the chimera-users or -dev lists for "community building" purposes, though I'll leave that up to your discretion. --Eric Begin forwarded message: > From: "Brady Bernard" <bradyb(a)u.washington.edu> > Date: January 11, 2007 5:06:21 PM PST > To: "Eric Pettersen" <pett(a)cgl.ucsf.edu> > Subject: chimera to rebuild crystal > > hi, > > i am interested in using distance-dependent statistics in a scoring > function and i would like more than the default 3x3x3 repeating units > to rebuild a crystal using cryst1 data in pdb files. how can i do > this with chimera? i will need to do this for thousands of files and > am familiar with scripting and using the -nogui option with cmd files, > etc. > > thanks in advance for your help, > > brady bernard > uw bioengineering

5 11

Chimera doesn't display AMBER molecular dynamics trajectories with periodic boundary condition.
by juyong Lee 16 Jan '07

16 Jan '07

Hi, I'm using chimera 1.2309 version. And I found out that MD movie module in chimera doesn't display AMBER trajectory file with periodic condition correctly. I works well only with non-periodic condition trajectory file. Another visualization program, VMD, has two seperated options for AMBER trajectory file: with periodic condition and not. I prefer display style of chimera. So, I really hope to see my AMBER trajectory with Chimera. Do you have any tips for this problem? or have plan to add the format, with periodic boundary condition. :-) Thanks again for your great program and have a nice day! ============================================= Lee, juyong Ph.D student, Department of chemistry, Seoul National University, Korea. drfaust23(a)gmail.com

2 2

Re: [Chimera-users] other/2169
by conrad＠cgl.ucsf.edu 16 Jan '07

16 Jan '07

Synopsis: interface with QPACK State-Changed-From-To: open->closed State-Changed-By: conrad State-Changed-When: Tue Jan 16 10:18:12 2007 State-Changed-Why: QPACK interface available as experimental feature. See http://www.cgl.ucsf.edu/chimera/experimental/experimental.html for more information. http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=2169&database=chime…

1 0

Re: [Chimera-users] Select atom by serial number.
by Jean Didier Pie Marechal 16 Jan '07

16 Jan '07

Hi Elaine and thank you very much for your help. I am pleased to see the selection specifications are OK. Coming back from the WE, I retried this selection on my structure and... it works perfect... For once, it seems I needed a reboot more than my desktop... My apologies for your waste of time. Regards, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdonyola (Barcelona) Tel: +34.935814988 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dijous, Gener 11, 2007 8:59 pm Assumpte: Re: [Chimera-users] Select atom by serial number. > > Hi JD, > We also tested Chimera 1.2309 on Windows, and these specifications > > work correctly. Example: > Command: sel @/serialNumber=232 > will select NZ of Lys 27 in chain A of the PDB entry 1zik. The > only > other thing I can think of (besides what was in the previous > message) > is to check if your PDB file is correctly formatted. The > ATOM/HETATM > serial number is supposed to be in columns 7-11 and right-justified. > Best, > Elaine > > On Jan 11, 2007, at 11:39 AM, Elaine Meng wrote: > > > Hi JD, > > You are using the correct specifications - both of your examples > > > should work. I tested both approaches in Chimera 1.2304 on Mac > OSX > > and they worked correctly. We'll have to look into your > specific > > version/platform and get back to you. If you want, you could > send > > me the PDB file you are using so I could test if there is some > > issue specific to that structure. To be clear: the serial > number > > is the number shown in the column after ATOM (or HETATM) in the > PDB > > file, regardless of what order the atoms are really in. That > is, > > if the first ATOM has 2 in that column, its serial number is 2 > and > > not 1. > > Best, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > > UCSF Computer Graphics Lab and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > > > > > > On Jan 11, 2007, at 10:47 AM, Jean-Didier Maréchal wrote: > > > >> Hi Everyone, > >> > >> > >> > >> > >> > >> I am desperately trying to select an atom of my pdb by its > serial > >> number. > >> > >> Looking at the archives, it seems that I should put something > like > >> @/serialNumber=525 > >> > >> I tried “sel #0@/serialNumber=525” in the commandl ine and “@/ > >> serialNumber=525” in the Atom Specifier. None of these > selections > >> worked. Can someone tell me the right way to do this, please ? > >> > >> > >> > >> Cheers > >> > >> JD > >> > >> > >> > >> Current running chimera: version 1 build 2309 > >> > >> OS: windows > >> > >> > >> > >> _______________________________________________ > >> Chimera-users mailing list > >> Chimera-users(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

1 0

Numeric/numpy revisited
by Randy Heiland 11 Jan '07

11 Jan '07

I'll post this long-winded thing to the users list although it's really for the developers... I'm revisiting the issue of wanting to have access to the numpy pkg (numpy.scipy.org) for a Chimera plugin - a delayed continuation of the problem discussed here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-April/000743.html Here's my situation: I installed chimera-1.2304-osx_x11.dmg. I then built the numpy pkg (from svn) using my system's python (2.4) via 'python setup.py build' and copied the resulting /numpy dir into the chimera /share dir. I then discover/verify 2 things: 1) using my system's python, I can successfully import both Numeric and numpy - Numeric coming from chimera and the numpy that I just built and copied into chimera's /share dir 2) using the python2.4 bundled with chimera, I cannot import both Numeric and numpy. I can always import one (either one), but then get a bizarre error when trying to import the other. --------------------------- More verbosely: I set PYTHONPATH to /Applications/Chimera.app/Contents/Resources/lib/python2.4/site-packages/Num eric:/Applications/Chimera.app/Contents/Resources/share Then check the system python: [macmini:~] heiland% pwd /Users/heiland [macmini:~] heiland% which python /usr/local/bin/python [macmini:~] heiland% ll /usr/local/bin/python lrwxr-xr-x 1 root heiland 68 Jul 27 06:19 /usr/local/bin/python@ -> ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/python [macmini:~] heiland% python Python 2.4.3 (#1, Apr 7 2006, 10:54:33) [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric >>> import numpy >>> from numpy.core.multiarray import typeinfo >>> Then check the chimera python: /Applications/Chimera.app/Contents/Resources/share [macmini:Contents/Resources/share] heiland% ../bin/python2.4 Python 2.4.3 (#1, Oct 16 2006, 09:43:37) [GCC 4.0.1 (Apple Computer, Inc. build 5247)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric >>> import numpy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Applications/Chimera.app/Contents/Resources/share/numpy/__init__.py", line 36, in ? import core File "numpy/core/__init__.py", line 8, in ? import numerictypes as nt File "numpy/core/numerictypes.py", line 83, in ? from multiarray import typeinfo, ndarray, array, empty, dtype ImportError: cannot import name typeinfo ----------------------------- OK, it then dawns on me that probably what I really should be doing is building numpy using chimera's python. So, after downloading the chimera (1.2318) OSX headers (http://www.cgl.ucsf.edu/chimera/sourcecode.html ), putting the /include in the /Resources dir, and doing: /Applications/Chimera.app/Contents/Resources/bin/python2.4 setup.py build It all builds fine, but then I have the same bizarre error when trying to import both Numeric and numpy as before. Crap. So I then use 'ldd' to see the dependencies in the different python executables: ldd /Applications/Chimera.app/Contents/Resources/bin/python2.4 /Applications/Chimera.app/Contents/Resources/bin/python2.4: /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 71.1.3) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 47.1.0) [macmini:~] heiland% ldd /Library/Frameworks/Python.framework/Versions/2.4/bin/python /Library/Frameworks/Python.framework/Versions/2.4/bin/python: /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 47.1.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.3) Note the different versions on the libSystem.B.dylib. Some more poking... [macmini:~] heiland% locate libgcc_s.1.dylib /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib [macmini:~] heiland% ldd /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3) [macmini:~] heiland% ldd /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 71.1.3) [macmini:~] heiland% ldd /usr/lib/libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.2) ----------------------------- One thing worth noting is the different gcc builds (my system python used a later build, 5250, cf 5247 for chimera's python). I also installed the latest xcode (2.4.1) before doing all this. If you've stayed with me to the end, I congratulate you :) Basic question - any ideas? Would it be possible for the Chimera OSX developers to verify they have the latest xcode? And secondly, do you know how one can the chimera python have the dependency on libSystem.B.dylib v.88.1.2 instead of 71.1.3 ? Thanks, -Randy Fwiw, this link http://mail.python.org/pipermail/pythonmac-sig/2006-April/017310.html seems related to this thread also.

2 1

Select atom by serial number.
by Jean-Didier Maréchal 11 Jan '07

11 Jan '07

Hi Everyone, I am desperately trying to select an atom of my pdb by its serial number. Looking at the archives, it seems that I should put something like @/serialNumber=525 I tried sel #0@/serialNumber=525 in the commandl ine and @/serialNumber=525 in the Atom Specifier. None of these selections worked. Can someone tell me the right way to do this, please ? Cheers JD Current running chimera: version 1 build 2309 OS: windows

2 2

secondary structure assignment
by nurul 10 Jan '07

10 Jan '07

hello i'm a student from malaysia and i'm using chimera in my studies, i have one question regarding this software, how does it assign the secondary structure? is it using dssp or stride or any other secondary structure assignment program? thank you

2 1

Chimera benchmarks in both OSX and WinXP on same hardware
by Jeff Speir 08 Jan '07

08 Jan '07

Dear Chimera developers, By request from my lab mates I've run Chimera's built-in benchmark routine under both OSX and Windows XP Pro SP2 for comparison. Attached is an MSWord document with the results. Hope they are useful. Of note, OSX falls behind in the ribbon graphics compared to WinXP, especially with large molecules. The test was done on an Apple Mac Pro (hardware details in attached document) with Windows XP Pro installed via Boot Camp. Both operating systems were fully updated with all available patches. Please let me know if you have any questions. Best Regards, Jeff Jeffrey A. Speir, Ph.D. The Scripps Research Institute Dept. of Molecular Biology 10550 North Torrey Pines Rd. La Jolla, CA 92037 Phone: (858) 784-8646 Fax: (858) 784-8660 E-mail: speir(a)scripps.edu

2 1

OSX headers
by Randy Heiland 04 Jan '07

04 Jan '07

Hi gang, Would it be possible to get the latest OSX (10.4) headers posted at http://www.cgl.ucsf.edu/chimera/sourcecode.html ? -Randy

2 1

command line zone selection?
by Kenward Vaughan 02 Jan '07

02 Jan '07

I'm putting together a demo for my students this next semester, and was hoping to be able to do a zone selection about the ligand. Is this possible with the command line? I haven't been able to pull out a reference for such, yet. Certainly I could pull together the list of residues myself, but thought it'd be nice to have the command available. Some students might like to create a demo file for their reports, and this would become a pivotal tool for a subset of those. If not directly available, then a wishlist addition, perhaps? Something like: zonesel [within|beyond] [+/- angstroms] [atom-spec] where the sign of the angstrom value denotes whether to include (+) or exclude (-) the atoms in atom-spec. Cheers, Kenward Vaughan -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$???

4 9

how to change the color and thickness of the unit cell outline
by Sabuj Pattanayek 02 Jan '07

02 Jan '07

Hi, How do I change the color and thickness of the unit cell outline? Thanks, Sabuj

2 1

Re: [Chimera-users] chimera and my ATI card
by Thomas Goddard 29 Dec '06

29 Dec '06

Hi Jeff, The system crash on your laptop indicates it is a graphics driver problem. Unfortunately these are very common -- maybe 1 in 20 driver version / graphics card combinations have Chimera crashing or system crashing bugs. I intend to make a web page that includes all the bad combinations we have encountered -- hopefully I'll get to it in January. The reason Chimera is particularly susceptible to these bugs is that it uses many capabilities of the OpenGL 3-d graphics library -- some that are seldom used by video games and other 3-d applications. There are only 4 practical solutions: 1) update the driver, 2) use an older driver, 3) set driver options to use less OpenGL acceleration, or 4) use a different machine. I use solution 2 on my home machine with an Nvidia Quadro driver that is a dozen versions behind the current one and over a year old. New drivers come out fairly often for both Nvidia and ATI cards and usually do not offer better performance -- only a new set of bugs (old ones fixed, new ones introduced). If you could send us a Chimera bug report by starting Chimera and use menu entry Help / Report a Bug this will send us your graphics driver version so we can include it on our bad drivers page. And if you find another driver version that works I would of course like to know which version. Sorry to offer so little help on this. Tom From: Jeff To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: chimera and my ATI card Date: Thu, 28 Dec 2006 23:59:26 -0800 hi Tom, on my laptop (IBM T43p), chimera is crashing the machine. I have the latest release installed in WinXP (as of 12/21), and a fairly recent release (within 2006) installed on Linux (also on same machine, different drive). this occurs with both really small volumes (100 cubed) and larger ones (600x400x100 or so), doing common tasks like rotating a surface rendering. in XP, it froze with a required reboot; with Linux, I got the screen that I have attached. the GPU is an 'ATI MOBILITY FireGL V3200', which was one of the GPUs you could get on a 'workstation laptop' back in June '05. I am pretty sure the drivers are current (within '06) and I use the ATI proprietary drivers in both XP and Linux - there is a standard ATI driver package that you download and then it just installs the proper version for your card. On an older laptop (prior to '05) I had similar issues with crashing, also on an ATI card, but different generation (was a Dell purchased in feb. '02). on my desktop workstation with an NVidia card, it works fine, although sometimes surfaces get rendered in the wrong place (something in background looks more in foreground, etc) - but I don't have problems with chimera getting killed (or killing the OS). any thoughts on having it run on my laptop? this machine is the only one I have access to outside of the lab, and was originally bought for this purpose (reconstructions and processing). thanks, -jeff

1 0

Flickering graphics
by Thomas Goddard 22 Dec '06

22 Dec '06

Hi Murali, What kind of flickering do you see when moving maps in Chimera? Does the surface appear shattered? One nvidia graphics driver bug I have seen causes the surface to appear broken into many triangles instead of smooth while it is moved. Or is it tearing that you see? That is when the top half of the screen momentarily shows one position for the map but the bottom shows a different one. That happens because you are moving the model and the redraw is not synchronized to the vertical refresh of the display. That is a graphics driver setting problem. Or does flicker mean it appears like every other frame is black? Every possibility I can think of points to a graphics driver problem, not a Chimera problem. You can check on Linux what graphics driver you are using with the glxinfo command: % glxinfo ... OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro4 500 GoGL/AGP/SSE2 OpenGL version string: 1.5.2 NVIDIA 66.29 ... The OpenGL renderer and version lines tell you the driver. If it says "Mesa" this means you have no driver installed and it is using software rendering (no hardware acceleration). Usually a new Linux system does not have a graphics driver installed by default so you have to get the driver from the NVidia web site. http://www.nvidia.com/content/drivers/drivers.asp The latest Nvidia GeForce driver version is 9746. The first step to try to fix your problem is update to the newest driver. Tom > Date: Fri, 22 Dec 2006 09:42:43 -0600 > From: "Murali Ayaluru" <mayaluru(a)gmail.com> > To: goddard(a)cgl.ucsf.edu > Subject: flickerings in model > > Hi, > > Greetings! > > I am using Chimera (chimera-1.2304-linux.exe) in Linux (FC-6) environment. > Basically I use this > for visualizing the structures generated from EM. While moving the model > (either vertical or horizontal) and also while rendering the volumes, I saw > lot of flickering in the model. Is there some parameter I have to change > to fix this problem? The graphic card we use is nVidia GeForce 7300 LE. I > don't have much experience in linux OS. Any suggestions to fix the problem > will be highly appreciated. > > Thanks and have a nice day. > > Regards, > Murali

1 0

Benchmark results
by Daniil Zaitsev 19 Dec '06

19 Dec '06

hi - here is benchmark result for new version of Chimera. Original benchmark progress log file is attached. Graphics NVidia GeForce Go 7200 Processor Intel Core Duo T2050 Clock (MHz) 533 OS Type Windows Surface 990 Mesh 368 Contour 148 Solid 173 Recolor 87 Notes Laptop Test Date 12/06 Chimera Version 2304 Machine HP Pavilion dv2000t Graphics Memory (Mb) 128 Main Memory (Mb) 1024 OS Version XP Home Driver Version 8.4.6.4

2 1

compressed versus gzipped Re: Read compressed PDB files -question, suggestion
by Moo Cow 12 Dec '06

12 Dec '06

A thousand pardons. You are right. I phrased the question wrongly. Chimera does open gzip'd files ( xx.gz). It does not open compress'd files (xx.Z). > You can also open gzipped files with Chimera's "open" command or as > an argument as you start Chimera. [...] > > You can use the Chimera File / Open... dialog to directly open a gzip > > PDB file. This was added to Chimera about one year ago. It does not work Why, you may ask, would anyone use compress these days ? If you mirror or rsync the protein data bank, they are still distributing files that have been squashed with compress and have a ".Z" extension. gunzip will happily eat and uncompress these files. I do not know how chimera handles compressed files. If it reads from a pipe, it might be nice to persuade it to feed .Z files to gunzip. I think it might be more difficult if chimera uses the python/zlib interface. Many thanks -- Search for products and services at: http://search.mail.com

2 1

SDF format
by Randy Heiland 12 Dec '06

12 Dec '06

Just wanted to ask about Chimera's support for reading in SDF formatted files, e.g. from PubChem. It seems not to be one of the supported formats. Obviously we can use a converter to get pdb format, but thought I'd ask the experts. Thanks, Randy

3 2

Transparent Ribbon
by Anna Feldman-Salit 12 Dec '06

12 Dec '06

Dear All, From some reason I cannot find the option of making ribbon representation transparent. Can you please give me a hint? Thanks a lot in advance, Anna

2 1

saving with angles
by Gabor Papai 12 Dec '06

12 Dec '06

Dear everybody, Is there a way in Chimera to save density maps when I rotate them with the modified angles? In practice, I use the 'fit map in map' to align two maps in respect to each other and I would like to save them for further analysis with different softwares. Therefore I would like to conserve their position (shift and rotation). Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

2 3

Delphi Controller
by sette＠uniroma2.it 11 Dec '06

11 Dec '06

Dear all, I have a simple question: does Delphi controller works under unix only or it is possible to work with it under Linux and/or Windows XP? Thanks a lot, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

5 4

Read compressed PDB files -question, suggestion
by Moo Cow 08 Dec '06

08 Dec '06

We store the PDB locally, but compressed. Can one persuade chimera to read coordinates from a pipe ? Maybe this could be done at the python level. It might also not be too hard to use the python binding to the zlib library, but I would not know how to do this. I imagine the interest (or not) would not be limited to reading PDB files. many thanks for any suggestions. -- Search for products and services at: http://search.mail.com

3 2

Apply the symmetry to the fitted models in map
by Hong-Wei Wang 06 Dec '06

06 Dec '06

Hi, Tom I remember you were showing docking a model into map with high symmetry (you showed the actomyosin filament example). I am wondering how you generate the symmetry in the docking and if the symmetry information is necessary for the correct fitting. Thanks a lot! Hongwei ----------------------------------- Hongwei Wang, Ph D MS 20A-355, LSD, LBNL 1 Cyclotron Rd, Berkeley, CA 94720 510-642-2222 (O) 510-642-8806 (FAX) hwwang(a)lbl.gov

2 1

volume viewer issue
by Matthew Shawkey 06 Dec '06

06 Dec '06

Hi, I am using chimera to visualize a stack of EM serial sections. I can load them into Chimera (as MRC file), but when I try to view the stack in the volume viewer w the "solids" option all I see is a white square.. w the mesh and surface options the stack shows up as a grainy image on which it's difficult to see any depth.. any suggestions? THanks, Matt

2 1

Uploading several trajectories for MDmovie
by Anna Feldman-Salit 04 Dec '06

04 Dec '06

Dear all, I would like to know if there is any possibility to sequentially upload several trajectories with MDmovie option (or command line) and then to visualize them with "no stop" in between. These trajectories were generated by AMBER with "restart" input files. Such an option happens to be in VMD, but it's more convenient for me to work with Chimera (I have Chimera1.2304). Thanks a lot in advance, Anna

2 1

Fit models to map
by hsosa＠aecom.yu.edu 04 Dec '06

04 Dec '06

I wonder how the "Fit models to map" function do the fitting. Does it find the best cross-correlation value between a 3D density calculated from the atomic model and the 3D density map?. What is the maximum displacements and rotations tested around the current position? What is the step size of the rotations/displacements? Thanks Regards Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

2 1

Re: [Chimera-users] inter-surface calculations in Chimera
by Elaine Meng 01 Dec '06

01 Dec '06

Hi Gali, Eric forwarded your question to me. The Intersurf tool generates a surface between the interacting molecules that is different from the surface of either molecule - it is mainly useful for viewing an interface and showing its properties (for example, with coloring by hydrophobicity or electrostatic potential), but not for measuring the surface area. It is possible to measure volume and surface area in Chimera, but currently it is a long process. We hope to have a simpler process available in the future. I'll describe two different approaches. (1) the simpler and more approximate way to calculate buried surface area and void volume in the complex: approx buried surface area = [(surface area of X) + (surface area of Y) - (surface area of XY)] / 2 approx interface void volume = (volume of XY) - (volume of X) - (volume of Y) The "Measure Volume and Area" tool can be used to calculate the surface areas and volumes. [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/ measurevol.html ] The trick is to first make a surface that encloses both X and Y and measure its values. Then, make surfaces that separately enclose X and Y and measure again. Here is a concrete example. PDB structure 1cf7 has two protein chains A and B, two DNA chains C and D, and some water. I'd open the structure and delete everything but the protein and DNA. command: open 1cf7 command: select :.a-d command: sel invert command: delete sel command: surfcat complex :.a-d command: surf complex Tools... Surface/Binding Analysis... Measure Volume and Area (measure values for the complex) command: surfcat protein :.a-b command: surf protein (choose the protein surface in Measure Volume and Area, compute again) command: surfcat dna :.c-d command: surf dna (choose the dna surface in Measure Volume and Area, compute again) Finally, use the equations above. All the results can be viewed in the Reply Log (under Favorites). These values are for molecular surfaces (also known as solvent-excluded, where the probe touches), not solvent-accessible (traced by the probe center). For this structure, I calculate approx 530 square angstroms surface area buried, approx 730 cubic angstroms of interface void volume. (2) A more detailed approach can yield different values for the areas buried on X and Y: (surface area of X buried in the XY interface) = (surface area from all atoms of X in surface enclosing XY) - (surface area from all atoms of X in surface enclosing just X) with a similar equation for Y. Currently, the only way to get atomic rather than total surface areas in Chimera is by using the "Area/Volume from Web" tool [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html ] which uses a Web server at NCBI and loads the atomic values into Chimera. Because the MSMS option of the server has problems with nucleic acids, the only choice for your complexes is to calculate solvent-accessible surface areas (not the solvent-excluded surface areas calculated by method (1) above). The main trick is to first send only XY to the server (making sure solvent, ions, etc. are NOT included). Then using Attribute Calculator, [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html ] sum the values for the atoms of X in that combined surface, and likewise get a total for Y. Then, delete everything except X and send it to the server again, getting the total for X alone. Close/reopen the structure, delete everything except Y, and send it to the server to get the total for Y alone. Subtract the value for X (Y) in the complex from the total for X (Y) alone. Here is a concrete example. PDB structure 1cf7 has two protein chains A and B, two DNA chains C and D, and some water. I'd open the structure and delete everything but the protein and DNA. command: open 1cf7 command: select :.a-d command: sel invert command: delete sel Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the protein and DNA command: select :.a-b Tools... Structure Analysis... Attribute Calculator calculate an attribute (name doesn't matter) for "models" with the Formula: sum(atom.accessibleSurface) with the option "Restrict formula domain to current selection" write down the total for A-B (which is the PROTEIN IN THE COMPLEX) (I get approx 7473) command: select :.c-d calculate an attribute (name doesn't matter) for "models" with the Formula: sum(atom.accessibleSurface) with the option "Restrict formula domain to current selection" write down the total for C-D (which is the DNA IN THE COMPLEX) (I get approx 4502) command: delete :.c-d now only the protein is left Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the protein - get the total for PROTEIN ALONE (Favorites... Reply Log) (I get approx 8842) command: close 0 command: open 1cf7 command: select :.c-d command: sel invert command: delete sel now only the DNA is left Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the DNA - get the total for DNA ALONE (Favorites... Reply Log) (I get approx 5758) Use the equation above to get the buried solvent-accessible surface areas. I calculate approx 1369 square angstroms buried for the protein, approx 1256 square angstroms buried for the DNA. You can't compare these solvent-accessible areas to the solvent-excluded areas calculated by method (1) ... the solvent-accessible values are generally much larger. PHEW! I congratulate everyone who got this far. The written explanation makes it seem longer than actually performing the process. I hope this helps, Elaine On Nov 30, 2006, at 7:35 AM, galig wrote: > Dear Eric, > > I have a small question regarding the calculation of inter-surfaces in > Chimera: > I have several protein/DNA complexes, and I would like to compare > their protein/DNA interfaces. I used Tools-->surface/binding > analysis-->compute interface surface and chose the protein and DNA > chains. the result, if I understand it correct, is per atom. Is there > a place to find the overall number representing the contact surface? > is this a different or similar calculation? > One more thing- how do I calculate the void intermolecular volume > between the chains? > > Thank you and sorry to bother you, > > Gali Golan > Dept. of Inorganic Chemistry > The Hebrew U. of Jerusalem > Jerusalem 91904 Israel > Tel. 972-2-6585610 > Fax 972-2-6585319 > ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

2 1

Re: [Chimera-users] Chimera on x86_64?
by Thomas Goddard 29 Nov '06

29 Nov '06

Hi Ben, There's no technical obstacle to us making regular 64-bit linux Chimera distributions. The only issue is having time to do it. The work involves compiling the ~30 third party libraries that Chimera uses. I did this is the past and it took about one day of fiddling. Our Chimera build scripts compile all of the third party libraries automatically and my past hand fiddling to build on 64-bit linux would have to be put into our scripts. That could take a 1 to 5 days of work. We have a 64-bit linux machine to do the work on. So it all comes down to when one of the 4 developers (Tom Goddard, Eric Pettersen, Greg Couch, or Conrad Huang) has time to work on that. I don't think I will have time until January at the earliest. Could you give me a better sense of how much need there is in the Sali lab? Are you really saying you would not install 32-bit Linux system libraries except for Chimera? I would think there are a fair number of applications out there with binary distributions only for 32-bit. The other problem you point out is that 32-bit Chimera Python cannot use your own 64-bit Python modules. Are you using additional C Python modules within Chimera that do not come with Chimera? That is interesting -- what are they? Tom > From: Ben Webb <ben(a)salilab.org> > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: Wed, 29 Nov 2006 12:51:27 -0800 > Subject: Chimera on x86_64? > > I wonder if you could give me a rough idea of when you plan to make > regular builds of Chimera on x86_64 (if at all)? All I've been able to > glean from the download page and the mailing list archive is that you > do make occasional builds, but recommend the 32-bit version. > > Memory isn't so much of an issue for us in particular (although we are > increasingly looking at large EM maps) but the requirement to have > 32-bit libraries is starting to become a problem. All of our new > desktops are x86_64 machines, and it's a pain to require the 32-bit > libraries just for Chimera. Additionally, our users want to > mix-and-match Python modules (including Modeller, of course) and > Chimera is unable to import any module which has a C backend, since > they're compiled for x86_64 and the Python interpreter in Chimera is > 32-bit. (Of course, we could recompile all of our other Python modules > for 32-bit, but that would cause problems with x86_64 apps.) > > If you need people to test x86_64 Chimera builds, we certainly have > some demanding users here to break them. ;) > > Ben > -- > ben(a)salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle

2 1

Multiple Volume Viewer Windows and saving PDB file
by Batsal Devkota 28 Nov '06

28 Nov '06

Hi, I am just wondering if there is any way that I can have two or more volume viewer windows open at the same time. I am comparing two density maps and to be able to change the threshold and color for both maps, without having to go back and forth in the same window, would be much easier and useful. Also, I recently fitted a pdb crystal structure into a density map but was not able to save it with relation to the density map (the feature which was available in previous releases). However, if I have multiple pdb files open then I can save the pdb file of my interest with respect to the map. Is there anyway to save a fitted pdb file with respect to a density map without opening other pdb files? Thank you, Batsal. -------------------------------------------------- Batsal Devkota Graduate Student, School of Biology GeorgiaInstitute ofTechnology Atlanta, GA 30332-0400

4 3

Stereo on the 1.2304 version
by Anna Feldman-Salit 28 Nov '06

28 Nov '06

Hello, Unfortunately, I'm facing with a problem of stereo option on the version 1.2304. I can see the stereo when I turn the "stereo" option on, but the quality of the picture is not of the best ones. The main picture is likely screened on background, while it's also impossible to focus on the frontal part. I was playing a bit with camera-viewing parameters, but nothing worked for me. Before, working with pymol I used the "swap sides" option, which helped a lot. I tested our stereo glasses with pymol's stereo option again and it works smoothly. Since I definitely prefer to work with chimera, I would appreciate if this problem would be solved somehow. Do you have any suggestions? Thank you in advance! Best, Anna

2 1

Re: [Chimera-users] Increase/decrease the sphere
by Eric Pettersen 28 Nov '06

28 Nov '06

I forgot to mention that if you want to control ball/stick size on a more permanent basis, you can use the New Molecule preferences (Favorites->Preferences) to set them for all new molecules you open. --Eric On Nov 27, 2006, at 9:21 PM, tuhin(a)iitk.ac.in wrote: > Thanks for your helpful suggestion, Eric. > > Regards, > TKP > >> Hi, >> Sphere size is the same as the atom's VDW radius. You can change >> atom radii with the "vdwdefine" command, or by selecting atoms and >> bringing up the Selection Inspector (click on the button at the lower >> right of the Chimera interface) and typing a new value into the >> "radius:" field. >> Ball and stick size are controlled on a per-model basis. Use the >> Model Panel (Favorites->Model Panel) and double-click on line with >> the model you want to control. A dialog listing the attributes of >> that model will come up. The "ball scale:" field controls the size >> of balls. It is a fraction that the VDW radius is multiplied by to >> get the ball size (default: 0.25). The "stick scale:" field controls >> stick size and also a fraction that sticks get multiplied by. The >> default stick radius is 0.2 angstroms and default stick scale is 1.0, >> so the final default radius is 0.2 angstroms. The help page for the >> attribute dialog describes why there are two numbers involved if you >> care, and also describes the other attributes if you're interested. >> >> --Eric >> Eric Pettersen >> UCSF Computer Graphics Lab >> pett(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu >> >> >> On Nov 27, 2006, at 6:56 AM, tuhin(a)iitk.ac.in wrote: >> >>> Dear Chimera users, >>> >>> Could anybody tell me whether there is a way in chimera to >>> increase/decrease the size of the spheres/ball-and-stick in atom >>> display >>> (Action-->Atoms/Bonds-->sphere...). The wireframe has an option in >>> "wire >>> width", is there something like that for the above two options ?? >>> >>> Waiting for yours suggestions. >>> Thanks in advance. >>> >>> Best, >>> TKP >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >

1 0

Control of the volume viewer from the command line
by Lukas Palatinus 28 Nov '06

28 Nov '06

Hello all, I am trying to make a movie showing an evolution of an electron density map during an iterative optimization. For each optimization step I have one density map as volume data in xplor format. I depict the maps using the volume viewer, where I can set the number and level of the isosurface thresholds as well as their color. However, each newly opened map opens with default threshold setting, which is not suitable for my purposes. I make the movie using a command file of the type: open density1.xplor movie record wait 10 movie stop close 0 open density2.xplor movie record wait 10 movie stop ... I would need to be able to control the properties of the isosurfaces of the newly opened map from the command line or from the script file, or find a way to preserve the properties set for the first map in all subsequently opened maps. The search in Chimera manual did not lead me anywhere. Could anyone give me a hint how to proceed? With best regards Lukas Lukas Palatinus Laboratoire de Cristallographie EPFL Lausanne Tel.: +41 (0)21 693 0639 mailto: palat(a)fzu.cz

2 1

Re: [Chimera-users] Get angles in degree out of Rotation matrix
by Thomas Goddard 27 Nov '06

27 Nov '06

Hi Michael, Perhaps you can compare the orientation between the exact symmetric placement of a chain and the actual position by measuring the translation and rotation angle needed to align the two. By rotation angle I mean that any rotation can be represented as a rotation about a single axis (which depends on the rotation). I do not understand what you mean by rotation angles about x, y and z axes. As I mentioned that depends on the order of the rotations and therefore is rarely used. In the Chimera match command or matchmaker tool the optimal rotation matrix is computed -- it is *not* decomposed into separate x, y and z rotations during that calculation. I suppose if your system has symmetry about the z axis you could ask what rotation about z best aligns a chain with the exact symmetric chain location. In other words, only a z-axis rotation rather then rotation about an arbitrary axis would be allowed. Chimera does not have code for that and I have never heard that number reported. If you spell out precisely what angle is needed I can give better advice on how to get it from Chimera. Tom > From: "Stohr, Michael" <stohr(a)uni-mainz.de> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Date: Mon, 27 Nov 2006 09:51:31 +0100 > Subject: AW: Get angles in degree out of Rotation matrix > > Hi Tom, > > Thanks a lot for your description. It does not fit completely my demand. I will rephrase my question, is there a simple way to determine the three angles between the two 3d-structures of two identical chains? The background is that my molecule is not absolutely symmetrical and I want to quantify the asymmetry. So, I want to be able to say, this angle between this two chains differs from ideal symmetry angle by X degrees for different directions (x, y, z). I thought the rotation matrix would be the way to do so, but it does not seem so. I've found a not very precise method by using the distance tool and trigonometric functions. Therefore, if there is no answer for my question it will be ok at first especially I have to finish my theses very soon. By the way, in which order does for example the tool match or matchmaker rotates a structure or is this not predictable? > > Thanks for your afford, > Michael

1 0

Increase/decrease the sphere
by tuhin＠iitk.ac.in 27 Nov '06

27 Nov '06

Dear Chimera users, Could anybody tell me whether there is a way in chimera to increase/decrease the size of the spheres/ball-and-stick in atom display (Action-->Atoms/Bonds-->sphere...). The wireframe has an option in "wire width", is there something like that for the above two options ?? Waiting for yours suggestions. Thanks in advance. Best, TKP

2 1

Re: [Chimera-users] DelPhi
by Elaine Meng 24 Nov '06

24 Nov '06

Hi Stefano, Oh I see - it appears to be a problem with the Mac DelPhi download. I tried getting this myself, and could not run the executable, with this error message (probably the same problem you had): meng% /Users/meng/Desktop/release1.1/exe/delphiMacOSX; exit dyld: /Users/meng/Desktop/release1.1/exe/delphiMacOSX can't open library: /opt/ibmcmp/lib/libxlf90.dylib (No such file or directory, errno = 2) Trace/BPT trap logout [Process completed] I'm not an expert at understanding these messages, but it looks like the executable is looking for some code library that is not there. If you could run the executable successfully, the next step would be to put it in your "path," so that just typing the name of the executable in a Mac Terminal window would run the program. That would allow DelPhiController to connect properly. You would also want to download the DelPhi "sample data" http://luna.bioc.columbia.edu/honiglab/software/DelPhi/data.tar.gz which has charge and radius parameter files that can be used with the program. Sadly, in our current situation, we cannot use the program. I do not have the programming expertise to fix this library problem, but if any of us figures it out, we will definitely let you know. If you do get a fix from the Honig lab, it would be great if you could let me (or chimera-users) know - probably several of us would like to use this software on a Mac. Sorry about the trouble, Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

3 3

DelPhi
by Stefano Ciurli 24 Nov '06

24 Nov '06

Hello, does anyone know how to implement the DelPhi algorithm into Chimera? I am using a Powerbook G4. Thanks a lot Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

2 1

fitting map into map
by Gabor Papai 24 Nov '06

24 Nov '06

Hi, Does anybody know if there is a way to calculate fitting of EM density map into another EM density map? I know how it goes with PDBs, but couldn't figure out how I can do it with maps. Thanks for help in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

2 4

question about using swapaa in Chimera
by Ng, David (NIH/NCI) [E] 22 Nov '06

22 Nov '06

Hi, I'm currently learning to use Chimera. I wish to look at specific amino acid mutations in CDKN2A for effects in conformational changes and changes in protein interactions with known partners. When I type the command "swapaa P #0:24" in chimera to mutate arginine 24 to proline in CDKN2A, I get an error message that says "Value error: No connectivity template for residue P" Can you help me with this issue? Thanks. David Ng, M.D. Staff Clinician

2 2

Re: [Chimera-users] Get angles in degree out of Rotation matrix
by Thomas Goddard 20 Nov '06

20 Nov '06

Hi Michael, It is not very common to specify a 3-dimensional rotation in terms of a x-axis rotation, y-axis rotation and z-axis rotation because this decomposition depends on the order of the x, y, and z rotations. If you rotate 90 degrees about the x-axis, then 90 about the y-axis you get a different orientation than if you do the y-axis rotation first followed by the x-axis rotation. Chimera has a routine to produce the rotation axis (a unit vector in 3-dimensions) and rotation angle about that vector corresponding to a 3x3 rotation matrix. You could use that in Chimera with some Python code. If you just want the rotation angle and don't need the axis then the formula is simple Tr(R) = 1 + 2*cos(theta) where Tr(R) = sum of rotation matrix diagonal elements so the rotation angle theta = arccos((Tr(R) - 1)/2) Below I give the Chimera C++ code that also computes the axis. There are corner cases handled by this code for 0 degree and 180 degree rotations. Tom void Xform::getRotation(Vector *axis, Real *angle) const { Real cosTheta = (rot[0][0] + rot[1][1] + rot[2][2] - 1) / 2; if (fuzzyEqual(cosTheta, 1)) { *angle = 0; (*axis)[0] = (*axis)[1] = 0; (*axis)[2] = 1; return; } if (!fuzzyEqual(cosTheta, -1)) { *angle = degrees(acos(cosTheta)); Real sinTheta = sqrt(1 - cosTheta * cosTheta); (*axis)[0] = (rot[2][1] - rot[1][2]) / 2 / sinTheta; (*axis)[1] = (rot[0][2] - rot[2][0]) / 2 / sinTheta; (*axis)[2] = (rot[1][0] - rot[0][1]) / 2 / sinTheta; return; } *angle = 180; if (rot[0][0] >= rot[1][1]) { if (rot[0][0] >= rot[2][2]) { // rot00 is maximal diagonal term (*axis)[0] = sqrt(rot[0][0] - rot[1][1] - rot[2][2] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[0]); (*axis)[1] = halfInverse * rot[0][1]; (*axis)[2] = halfInverse * rot[0][2]; } else { // rot22 is maximal diagonal term (*axis)[2] = sqrt(rot[2][2] - rot[0][0] - rot[1][1] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[2]); (*axis)[0] = halfInverse * rot[0][2]; (*axis)[1] = halfInverse * rot[1][2]; } } else { if (rot[1][1] >= rot[2][2]) { // rot11 is maximal diagonal term (*axis)[1] = sqrt(rot[1][1] - rot[0][0] - rot[2][2] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[1]); (*axis)[0] = halfInverse * rot[0][1]; (*axis)[2] = halfInverse * rot[1][2]; } else { // rot22 is maximal diagonal term (*axis)[2] = sqrt(rot[2][2] - rot[0][0] - rot[1][1] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[2]); (*axis)[0] = halfInverse * rot[0][2]; (*axis)[1] = halfInverse * rot[1][2]; } } }

1 0

Re: [Chimera-users] suggestion
by Thomas Goddard 20 Nov '06

20 Nov '06

Hi David, Thanks for your suggestion to add coloring of isosurfaces based on gradient magnitude to Chimera. I think I can add this to the Surface Color tool in an hour or two since the gradient calculation code is already in Chimera (for fitting atomic models in maps). I'll try to put it in soon and send you the code to test. Description of coloring from article: "OpenDX (www.opendx.org) module MAKROVIS was implemented to create masks of different shapes and to analyze disorder in the reconstructions (Figure 1B). For this, isosurface rendering of a given voxel was colored as a function of the maximum density difference between the voxel and its neighbors." Tom > From: "David G. Morgan" <dmorgan(a)ucdavis.edu> > To: goddard(a)cgl.ucsf.edu > Subject: suggestion > Date: Thu, 16 Nov 2006 19:03:50 -0800 > > Tom, > > I have a suggestion for the developers "list of ideas to implement," if > you think there would be enough interest from users and that it is > something that chimera should do. I realize that you get lots of > suggestions, and that some of them are simply outside the realm of what > the chimera developers think chimera is intended to do. But since you > do ask for suggestions, here's my most recent one. > > I'm attaching a recent journal article where the authors used a color > coding scheme to display "order/disorder" regions of an EM > reconstruction. The images are in Fig 1 B and the rather sparse > description of the "algorithm" is a single sentence in the "Image > Processing 3D Reconstruction" section (p 1046). The idea of color > coding some estimate of the better defined regions of a density map is > very nice (and clever), and would be extremely helpful in lots of > situations (my plug for wanting you guys to implement something > similar...). > > The idea behind this is that for any given region of iso-surface, the > density gradient normal to that surface should be a reasonable measure > of how well defined the density is. In other words, a very steep > gradient (e.g., a fast transition between protein and solvent) means > very well defined density and a flat gradient means weakly defined > density (disordered regions, partial occupancy, etc.). The authors > don't do such a complicated calculation, but it seems that what they > implemented at least captures most of this sort of character. > > I think the key to this is that the gradient is calculated "locally." > I've looked at gradients as a function of resolution with the idea of > using it to help chose a proper iso-surface. While it works well with > model data, real reconstructions aren't nearly so well behaved. I > hadn't thought about this in a while, but I think what the authors have > done both helps explain the behavior of my real data (the gradient is > simply too varied) and is a quite useful visualization tool. > > So please think about implementing something like this in the volume > handling tools of chimera. > > David Gene Morgan > Advanced Microscopy & Proteomics > Molecular & Cellular Biology > University of California at Davis > 530 752 2693 (lab) > 530 752 3085 (FAX) > ---- > removed PDF for > > Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD, Butcher SJ. > Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging. > Structure. 2006 Jun;14(6):1039-48.

1 1

Duplicate Atom Serial Numbers
by Albion Baucom 17 Nov '06

17 Nov '06

When I generate a PDB file, and generate symmetry related biological units, I frequently replicate the single structure. When I do this the atoms numbers get duplicated and when I open the structure in Chimera it prints to the screen warning: duplicate atom serial number found: NNNN where NNNN is the duplicate number. The problem with this is it slows down opening the file by a huge factor. I assume that the print statement to the terminal is adding a lot of time to the file reading process. Is there any way around this, or a way to simply turn this off? I am not concerned with the specifics of the duplicate atom numbers. A single error message to alert me the fact that there are duplicate atoms would be enough. Once Chimera is done reading the structure it works fine. Rotations are smooth. Displaying ribbons is quick, etc. This doesn't appear to be a slow down due to atom limitations, but simply the overhead of printing that error message over and over to the console. Of course I am aware that there are BIOMT records to generate symmetry related molecules using a single repeating unit, or I could generate separate PDB files for each repeating unit, but this is a lot more work and bookkeeping when I can use some existing simple programs to simply rotate and translate a single set of coordinates. Thanks Albion

3 4

deleting model memories
by wendy ochoa 15 Nov '06

15 Nov '06

Is there a way to delete model memories in the emanimator option? thanks a lot wendy

3 2

Question about molecular surface generation
by Nihshanka Debroy 15 Nov '06

15 Nov '06

Hi Chimera users, I have been generating molecular surfaces for several proteins and am hoping to perform some matrix calculations on the points where the surfaces are being calculated. So I was wondering if there is a way to reduce the # points where the surface is calculated/plotted, as that would really reduce the dimensions of my matrices! I am using the Delphi Controller to generate electrostatic potentials. My understanding of Delphi is that it finds finite difference solutions to the Poisson Boltzmann equation by mapping the system onto a grid of points. After the potentials are calculated at those grid points, when generating the potentials on the molecular surface, interpolation is used to calculate the potentials for locations on the molecular surface that are between points on the grid used in Delphi. So I don't think its the grid size for Delphi that I need to be reducing, but the # points where the actual molecular surface is calculated. Is it possible to reduce this number somewhere in the code files? Thanks a lot! Sincerely, Nihshanka

2 1

MultiAlign viewer
by Mireille Krier 14 Nov '06

14 Nov '06

Dear all, I want to add to the header of a sequence alignment graphical representations such as cylinders and thick arrows to symbolize stretches of helix and strand. Is this possible? Should one annotate this in the Stockholm format file (and if yes could you provide me an example file) ? Cheers, Mireille

2 1

About electrostatic potentials
by xiaobinfan＠tju.edu.cn 14 Nov '06

14 Nov '06

Dear Sir/Madam: Thank you for reading. I am a new Chimera's user in China. I wonder whether the surface of a virus opened by Chimera could be colored by its electrostatic potentials calculated by the DelPhiController. I can color the surface of a small protein on Linux platform now. However, the surface of a whole virus (PDB 1ny7) opened by the Multiscale Models could not. Does it possible to do that? Thank you for your support. Best wishes! Sincerely, Xiaobin Fan ---------------------------

2 1

Fwd: longbond and session restore problems
by Elaine Meng 14 Nov '06

14 Nov '06

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: November 14, 2006 10:36:35 AM PST > To: jean-francois menetret <menetret(a)bu.edu> > Cc: Eric Pettersen <pett(a)cgl.ucsf.edu>, Thomas Goddard > <goddard(a)cgl.ucsf.edu>, Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] longbond and session restore problems > > Hi Jean-Francois, > In my tests I didn't have this problem; showing Pipes-and-Planks > should not change which atoms and bonds are shown. > > However, I might understand what is happening: when you show the > "chain trace" of CA atoms only, a connection across the missing > part is shown even after you use "~longbond". This CA connection > line is different than the "missing segments" pseudobonds: > > -CA-CA-------CA-CA- > is the chain trace, not affected by ~longbond > > -N-CA-C- - - -N-CA-C- > is the backbone showing "real bonds" except for the pseudobond, > which is affected by ~longbond > > If you are showing just the CA atoms and you don't want the > connection, here are some possibilities: > (1) just hide all the CA atoms (for example, command: ~disp @ca) > OR > (2) change from "chain trace" (the CA atoms) to "backbone > only" (N,CA,C) - if you used ~longbond the connection will be gone > OR > (3) if you really wanted to keep showing just the CA atoms, you can > select each long CA-CA bond (which is also a pseudobond, although > not shown with a dashed line) with Ctrl-click, and use the > Selection Inspector to undisplay it. This tool is opened by > clicking the button on the lower right of the Chimera window. In > the Inspector, change to Inspect [Pseudobond] and change the > "displayed" attribute to "false." > > I hope this helps, > Elaine > > On Nov 14, 2006, at 6:51 AM, jean-francois menetret wrote: > >> Hi Elaine, >> >> thank you for your message >> I still have one problem with the long bonds, though : there >> reappear in pipes-and-plancks. >> About restoring a session, I agree, it was not an issue with the >> chimera version but with the speed/memory of my PC. Although >> chimera could save the session, it couldn't reopen it on my PC but >> it did on a faster one. >> >> Best wishes >> >> Jean-François Ménétret, PhD >> Boston University School of Medicine >> Physiology and Biophysics Department >> 700 Albany Street W315 >> Boston, MA 02118 >> Email: menetret(a)bu.edu >> Mailing address: 715 Albany Street > > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html >

1 0

longbond and session restore problems
by Thomas Goddard 09 Nov '06

09 Nov '06

Here are two problems reported by Jean-Francois Menetret in Chimera 2304 and 2306. ------- Start of forwarded message ------- Date: Thu, 9 Nov 2006 16:38:58 -0500 (EST) From: jean-francois menetret <menetret(a)bu.edu> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: problems report Hi Thomas, I have two problems to report 1) the longbond command doesn't seem to work (with chimera 2304 or 2306) 2) I saved a session under chimera 2304 but couldn't open it after=20 upgrading to 2306 Jean-Francois Jean-Fran=E7ois M=E9n=E9tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street ------- End of forwarded message -------

2 1

Re: [Chimera-users] Fwd: Chimera crashes with MacPro show solid
by Thomas Goddard 09 Nov '06

09 Nov '06

Peter EngelHardt replies about solid rendering crash on Mac. ------- Start of forwarded message ------- Date: Thu, 9 Nov 2006 22:42:41 +0300 To: Thomas Goddard <goddard(a)cgl.ucsf.edu> From: Peter Engelhardt <engelhar(a)medi.mappi.helsinki.fi> Subject: Re: [Chimera-users] Fwd: Chimera crashes with MacPro show solid Dear Tom, Thanks, I did what you told and it all worked out very fine Though a bit buggy - volumes disappear and appear suddenly - but under certain control anyhow. Cheers and thanks again Peter > The crash with solid rendering is almost surely a graphics driver bug. >The solid rendering code works correctly on many different graphics cards >and there is nothing in that code that works differently for stereo >rendering. > > Does the crash occur for solid rendering without stereo? yes instantly > > Does the size of the data set matter? not tested > > There are two solid rendering options that may avoid this crash. >These are shown in the volume dialog using the Features / Solid Rendering >Options menu entry. From the back trace you sent I see the crash occurs >when pushing the data to the graphics card and mapping the colors using >a colormap. If you turn off the option "Use colormap of size X for solids" >then different code will be used -- colors will be computed on the CPU >instead of on the graphics card. A second change that may avoid the >crash is turning off "Solids using 2D textures". This makes Chimera use >3 dimensional textures instead of 2 dimensional textures. > > Tom - -- ___________________________________________________________ Peter Engelhardt, PhD, docent Assistant Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology and Virology Haartman Institute P.O.Box 21, FI-00014 Univ. of Helsinki, Finland Visiting Address: Haartmaninkatu 3, Helsinki ------- End of forwarded message -------

1 0

Fwd: Chimera crashes with MacPro show solid
by Peter Engelhardt 09 Nov '06

09 Nov '06

In our Mac Pro Quad-Core 2.66GHz CTO Processor: 2.66 GHz Quad Xeon RAM 4G and NVIDIA Quadro FX 4500 512MB SDRAM, using Crystal Eyes Stereo Stereo works with iso surface and mesh but: CRASHES with show solid? Peter PS Following errors were reported and fwd to apple. >Date/Time: 2006-11-07 17:17:49.047 +0200 >OS Version: 10.4.8 (Build 8L2127) >Report Version: 4 > >Command: python2.4 >Path: /Applications/Chimera.app/Contents/Resources/bin/python2.4 >Parent: WindowServer [55] > >Version: 1.2303 (1.2303) > >PID: 457 >Thread: 0 > >Exception: EXC_BAD_ACCESS (0x0001) >Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x000000a4 > >Thread 0 Crashed: >0 libGLImage.dylib 0x940a3fc4 glgProcessColor(GLDPixelMode >const*, GLGOperation const*, unsigned long) + 46870 >1 libGLImage.dylib 0x940972aa glgProcessPixels + 296 >2 com.apple.GeForceFXGLDriver 0x028b4f1e gldGetTextureLevel + 10243 >3 GLEngine 0x02732062 glTexSubImage2D_Exec + 1633 >4 libGL.dylib 0x92b0edaa glTexSubImage2D + 139 >5 _volume.so 0x037fb30f Texture_2d::fill(unsigned >short*) + 147 >6 _volume.so > 0x037fb424 Texture_Plane::fill_texture() >+ 76 >7 _volume.so 0x037fb627 >Volume_Renderer_2DT::update_colormap_textures(int) + 159 >8 _volume.so 0x037fd865 >Volume_Renderer_2DT::update_texture_planes(int) + 567 >9 _volume.so > 0x037fd9d8 Volume_Renderer_2DT::draw() + >122 >10 _chimera.dylib > 0x0101c5f8 chimera::LensModel::xformDraw >(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const + 572 >11 _chimera.dylib 0x010190e1 chimera::Lens::draw >(chimera::LensViewer const*, chimera::LensViewer::DrawPass, int const*) + >241 >12 _chimera.dylib 0x01020e98 >chimera::LensViewer::drawScreenBoxes(otf::Array<int, (unsigned long)4> >const&, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, >std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >, >__gnu_cxx::__normal_iterator<chimera::ScreenBox*, >std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >) >const + 1024 >13 _chimera.dylib 0x01022674 chimera::LensViewer::draw >(bool) const + 460 >14 _chimera.dylib > 0x0101dd34 chimera::LensViewer::displayCB >(_object*) + 90 >15 _chimera.dylib 0x01095323 LensViewer_displayCB + 43 >16 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >17 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >18 python2.4 0x000b89dc builtin_apply + 201 >(bltinmodule.c:100) >19 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >20 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >21 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >22 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >23 python2.4 0x0000c662 instancemethod_call + 401 >(classobject.c:2447) >24 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >25 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >26 _tkinter.so 0x016efea4 PythonCmd + 220 (_tkinter.c: >2001) >27 libtcl8.4.dylib 0x0a00d10f TclInvokeStringCommand + 121 >28 libtcl8.4.dylib 0x0a00fa41 TclEvalObjvInternal + 769 >29 libtcl8.4.dylib 0x0a010694 Tcl_EvalObjv + 232 >30 libTogl2.0.dylib 0x0255d047 Togl_CallCallback + 144 >31 libTogl2.0.dylib 0x0255d235 Togl_Render + 46 >32 libtcl8.4.dylib 0x0a0648a9 TclServiceIdle + 65 >33 libtcl8.4.dylib 0x0a055661 Tcl_DoOneEvent + 380 >34 libtk8.4.dylib 0x0b00ae3a Tk_UpdateObjCmd + 44 >35 libtcl8.4.dylib 0x0a00fa41 TclEvalObjvInternal + 769 >36 libtcl8.4.dylib 0x0a010694 Tcl_EvalObjv + 232 >37 _tkinter.so > 0x016f18ad Tkapp_Call + 199 (_tkinter.c: >1314) >38 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >39 python2.4 0x000638b1 PyEval_EvalFrame + 23100 >(ceval.c:3645) >40 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >41 python2.4 0x0006370c PyEval_EvalFrame + 22679 >(ceval.c:3656) >42 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >43 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >44 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >45 python2.4 0x000617c2 PyEval_EvalFrame + 14669 >(ceval.c:3840) >46 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >47 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >48 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >49 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >50 python2.4 0x000b89dc builtin_apply + 201 >(bltinmodule.c:100) >51 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >52 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >53 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >54 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >55 python2.4 0x0000c662 instancemethod_call + 401 >(classobject.c:2447) >56 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >57 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >58 _tkinter.so 0x016efea4 PythonCmd + 220 (_tkinter.c: >2001) >59 libtcl8.4.dylib 0x0a00d10f TclInvokeStringCommand + 121 >60 libtcl8.4.dylib 0x0a00fa41 TclEvalObjvInternal + 769 >61 libtcl8.4.dylib 0x0a00fd57 Tcl_EvalEx + 503 >62 libtcl8.4.dylib 0x0a064f95 AfterProc + 106 >63 libtcl8.4.dylib 0x0a06477b TimerHandlerEventProc + 94 >64 libtcl8.4.dylib 0x0a055366 Tcl_ServiceEvent + 131 >65 libtcl8.4.dylib 0x0a05558f Tcl_DoOneEvent + 170 >66 _tkinter.so 0x016ef69f Tkapp_MainLoop + 188 >(_tkinter.c:2539) >67 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >68 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >69 python2.4 0x0006370c PyEval_EvalFrame + 22679 >(ceval.c:3656) >70 python2.4 0x000638b1 PyEval_EvalFrame + 23100 >(ceval.c:3645) >71 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >72 python2.4 0x0006370c PyEval_EvalFrame + 22679 >(ceval.c:3656) >73 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >74 python2.4 > 0x0006450a PyEval_EvalCode + 87 (ceval.c: >490) >75 python2.4 0x0008af5c PyRun_FileExFlags + 200 >(pythonrun.c:1265) >76 python2.4 > 0x0008b23f PyRun_SimpleFileExFlags + 640 >(pythonrun.c:860) >77 python2.4 0x00005974 Py_Main + 3199 (main.c:493) >78 python2.4 0x00001cc6 _start + 216 >79 python2.4 0x00001bed start + 41 > >Thread 1: >0 libSystem.B.dylib 0x90019d3c select + 12 >1 libSystem.B.dylib 0x90023d87 _pthread_body + 84 > >Thread 0 crashed with X86 Thread State (32-bit): > eax: 0x00000002 ebx: 0x940988bf ecx: 0x00000000 edx: 0x00000001 > edi: 0x00000000 esi: 0x608d1000 ebp: 0xbfffba68 esp: 0xbfffb720 > ss: 0x0000001f efl: 0x00010246 eip: 0x940a3fc4 cs: 0x00000017 > ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 > >Binary Images Description: > 0x1000 - 0xd2fff python2.4 /Applications/Chimera.app/Contents/ >Resources/bin/python2.4 > 0x392000 - 0x394fff libtr.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libtr.dylib > 0x3d8000 - 0x3dafff operator.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/operator.so > 0x3e4000 - 0x3e4fff _weakref.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_weakref.so > 0x3f0000 - 0x3f0fff _chimera.so /Applications/Chimera.app/Contents/ >Resources/lib/_chimera.so > 0x3f9000 - 0x3fbfff libwrappy2.dylib /Applications/Chimera.app/ >Contents/Resources/lib/libwrappy2.dylib > 0x505000 - 0x585fff libotf.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libotf.dylib > 0x5a8000 - 0x5b0fff libXext.6.dylib /usr/X11R6/lib/libXext.6.dylib > 0x5cd000 - 0x5ddfff libz.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libz.dylib > 0x5e5000 - 0x5e8fff strop.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/strop.so > 0x5f5000 - 0x5f6fff MacOS.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/MacOS.so > 0x705000 - 0x711fff libftgl.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libftgl.dylib > 0x1008000 - 0x11b5fff _chimera.dylib /Applications/Chimera.app/ >Contents/Resources/lib/_chimera.dylib > 0x1300000 - 0x1340fff libfreetype.6.dylib > /Applications/Chimera.app/Contents/Resources/lib/libfreetype.6.dylib > 0x148b000 - 0x14e6fff libGLU.1.dylib /usr/X11R6/lib/libGLU.1.dylib > 0x1511000 - 0x156bfff libGL.1.dylib /usr/X11R6/lib/libGL.1.dylib > 0x159f000 - 0x165cfff libX11.6.dylib /usr/X11R6/lib/libX11.6.dylib > 0x1684000 - 0x16bcfff _vrml.so /Applications/Chimera.app/Contents/ >Resources/lib/_vrml.so > 0x16ec000 - 0x16f2fff _tkinter.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_tkinter.so > 0x1707000 - 0x1708fff math.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/math.so > 0x1710000 - 0x1711fff _random.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_random.so > 0x17f9000 - 0x17f9fff _imagingtk.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/PIL/_imagingtk.so > 0x2048000 - 0x204afff binascii.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/binascii.so > 0x2054000 - 0x2055fff fcntl.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/fcntl.so > 0x205d000 - 0x20a1fff _imaging.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/PIL/_imaging.so > 0x2133000 - 0x2136fff array.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/array.so > 0x2176000 - 0x2177fff _ssl.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_ssl.so > 0x220f000 - 0x2215fff _socket.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_socket.so > 0x222a000 - 0x222bfff time.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/time.so > 0x2275000 - 0x2276fff cStringIO.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/cStringIO.so > 0x2300000 - 0x232ffff libTix8.4.dylib /Applications/Chimera.app/ >Contents/Resources/lib/Tix8.4/libTix8.4.dylib > 0x250d000 - 0x2529fff GLDriver /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Resources/GLDriver.bundle/GLDriver > 0x2530000 - 0x2554fff GLRendererFloat /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat > 0x255b000 - 0x2561fff libTogl2.0.dylib /Applications/Chimera.app/ >Contents/Resources/lib/Togl2.0/libTogl2.0.dylib > 0x2568000 - 0x2576fff libXmu.6.dylib /usr/X11R6/lib/libXmu.6.dylib > 0x257e000 - 0x25b7fff libXt.6.dylib /usr/X11R6/lib/libXt.6.dylib > 0x25cb000 - 0x25cffff libSM.6.dylib /usr/X11R6/lib/libSM.6.dylib > 0x25d4000 - 0x25e3fff libICE.6.dylib /usr/X11R6/lib/libICE.6.dylib > 0x2705000 - 0x285efff GLEngine /System/Library/Frameworks/ >OpenGL.framework/Resources/GLEngine.bundle/GLEngine > 0x288a000 - 0x29fafff com.apple.GeForceFXGLDriver 1.4.40 (4.4.0) > /System/Library/Extensions/GeForceFXGLDriver.bundle/Contents/MacOS/ >GeForceFXGLDriver > 0x2b9b000 - 0x2b9cfff _collaboratory.so > /Applications/Chimera.app/Contents/Resources/lib/_collaboratory.so > 0x2c99000 - 0x2c9cfff _AE.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_AE.so > 0x2caf000 - 0x2cb0fff _Evt.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_Evt.so > 0x2cbe000 - 0x2cc0fff struct.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/struct.so > 0x2cd8000 - 0x2cdefff _File.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_File.so > 0x2e1f000 - 0x2e22fff _Res.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_Res.so > 0x33b2000 - 0x33b3fff collections.so /Applications/Chimera.app/ >Contents/Resources/lib/python2.4/lib-dynload/collections.so > 0x3505000 - 0x3509fff multiarray.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/multiarray.so > 0x3519000 - 0x3529fff _numpy.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/_numpy.so > 0x355e000 - 0x356afff umath.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/umath.so > 0x35d9000 - 0x3688fff lapack_lite.so /Applications/Chimera.app/ >Contents/Resources/lib/python2.4/site-packages/Numeric/lapack_lite.so > 0x3791000 - 0x3797fff ranlib.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/ranlib.so > 0x37ee000 - 0x380efff _volume.so /Applications/Chimera.app/Contents/ >Resources/lib/_volume.so > 0x386e000 - 0x3891fff _surface.so /Applications/Chimera.app/Contents/ >Resources/lib/_surface.so > 0x3961000 - 0x3974fff _contour.so /Applications/Chimera.app/Contents/ >Resources/lib/_contour.so > 0xa000000 - 0xa081fff libtcl8.4.dylib /Applications/Chimera.app/ >Contents/Resources/lib/libtcl8.4.dylib > 0xb000000 - 0xb0a9fff libtk8.4.dylib /Applications/Chimera.app/ >Contents/Resources/lib/libtk8.4.dylib >0x8fe00000 - 0x8fe49fff dyld 46.9 /usr/lib/dyld >0x90000000 - 0x9016ffff libSystem.B.dylib > /usr/lib/libSystem.B.dylib >0x901bf000 - 0x901c1fff libmathCommon.A.dylib > /usr/lib/system/libmathCommon.A.dylib >0x901c3000 - 0x90200fff com.apple.CoreText 1.1.1 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/CoreText.framework/Versions/A/CoreText >0x90227000 - 0x902fcfff ATS /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/ >A/ATS >0x9031c000 - 0x90770fff com.apple.CoreGraphics 1.258.38 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics >0x90807000 - 0x908cffff com.apple.CoreFoundation 6.4.6 (368.27) > /System/Library/Frameworks/CoreFoundation.framework/Versions/A/ >CoreFoundation >0x9090d000 - 0x9090dfff com.apple.CoreServices 10.4 (???) > /System/Library/Frameworks/CoreServices.framework/Versions/A/ >CoreServices >0x9090f000 - 0x90a02fff libicucore.A.dylib > /usr/lib/libicucore.A.dylib >0x90a52000 - 0x90ad1fff libobjc.A.dylib /usr/lib/libobjc.A.dylib >0x90afa000 - 0x90b5efff libstdc++.6.dylib > /usr/lib/libstdc++.6.dylib >0x90bcd000 - 0x90bd4fff libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib >0x90bd9000 - 0x90c4cfff com.apple.framework.IOKit 1.4.6 (???) > /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit >0x90c61000 - 0x90c73fff libauto.dylib /usr/lib/libauto.dylib >0x90c79000 - 0x90f1ffff com.apple.CoreServices.CarbonCore 682.15 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >CarbonCore.framework/Versions/A/CarbonCore >0x90f62000 - 0x90fcafff com.apple.CoreServices.OSServices 4.1 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >OSServices.framework/Versions/A/OSServices >0x91003000 - 0x91041fff com.apple.CFNetwork 129.18 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >CFNetwork.framework/Versions/A/CFNetwork >0x91054000 - 0x91064fff com.apple.WebServices 1.1.3 (1.1.0) > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >WebServicesCore.framework/Versions/A/WebServicesCore >0x9106f000 - 0x910eefff com.apple.SearchKit 1.0.5 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >SearchKit.framework/Versions/A/SearchKit >0x91128000 - 0x91146fff com.apple.Metadata 10.4.4 (121.36) > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >Metadata.framework/Versions/A/Metadata >0x91152000 - 0x91160fff libz.1.dylib /usr/lib/libz.1.dylib >0x91163000 - 0x91302fff com.apple.security 4.5.1 (29002) > /System/Library/Frameworks/Security.framework/Versions/A/Security >0x91400000 - 0x91408fff com.apple.DiskArbitration 2.1.1 > /System/Library/Frameworks/DiskArbitration.framework/Versions/A/ >DiskArbitration >0x9140f000 - 0x91435fff com.apple.SystemConfiguration 1.8.6 > /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/ >SystemConfiguration >0x91447000 - 0x9144efff libbsm.dylib /usr/lib/libbsm.dylib >0x91452000 - 0x914c8fff com.apple.audio.CoreAudio 3.0.4 > /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio >0x91519000 - 0x91519fff com.apple.ApplicationServices 10.4 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >ApplicationServices >0x9151b000 - 0x91547fff com.apple.AE 314 (313) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/AE.framework/Versions/A/AE >0x9155a000 - 0x9162efff com.apple.ColorSync 4.4.8 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/ColorSync.framework/Versions/A/ColorSync >0x91669000 - 0x916dcfff com.apple.print.framework.PrintCore 4.6 (177.13) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/PrintCore.framework/Versions/A/PrintCore >0x9170a000 - 0x917b3fff com.apple.QD 3.10.21 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/QD.framework/Versions/A/QD >0x917d9000 - 0x91824fff com.apple.HIServices 1.5.2 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/HIServices.framework/Versions/A/HIServices >0x91843000 - 0x91859fff com.apple.LangAnalysis 1.6.3 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis >0x91865000 - 0x91880fff com.apple.FindByContent 1.5 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/FindByContent.framework/Versions/A/FindByContent >0x9188b000 - 0x918c8fff com.apple.LaunchServices 181 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/LaunchServices.framework/Versions/A/LaunchServices >0x918dc000 - 0x918e8fff com.apple.speech.synthesis.framework 3.5 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis >0x918ef000 - 0x9192afff com.apple.ImageIO.framework 1.5.0 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/ImageIO.framework/Versions/A/ImageIO >0x9193c000 - 0x919eefff libcrypto.0.9.7.dylib > /usr/lib/libcrypto.0.9.7.dylib >0x91a34000 - 0x91a4afff libcups.2.dylib /usr/lib/libcups.2.dylib >0x91a4f000 - 0x91a6dfff libJPEG.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libJPEG.dylib >0x91a72000 - 0x91ad0fff libJP2.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libJP2.dylib >0x91ae2000 - 0x91ae6fff libGIF.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libGIF.dylib >0x91ae8000 - 0x91b65fff libRaw.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libRaw.dylib >0x91b69000 - 0x91ba6fff libTIFF.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libTIFF.dylib >0x91bac000 - 0x91bc6fff libPng.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libPng.dylib >0x91bcb000 - 0x91bcdfff libRadiance.dylib > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib >0x91bcf000 - 0x91bcffff com.apple.Accelerate 1.3.1 (Accelerate 1.3.1) > /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate >0x91bd1000 - 0x91c5ffff com.apple.vImage 2.5 > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ >vImage.framework/Versions/A/vImage >0x91c66000 - 0x91c66fff com.apple.Accelerate.vecLib 3.3.1 (vecLib 3.3.1) > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ >vecLib.framework/Versions/A/vecLib >0x91c68000 - 0x91cc1fff libvMisc.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libvMisc.dylib >0x91cca000 - 0x91ceefff libvDSP.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libvDSP.dylib >0x91cf6000 - 0x920fffff libBLAS.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libBLAS.dylib >0x92139000 - 0x924edfff libLAPACK.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libLAPACK.dylib >0x9251a000 - 0x92597fff com.apple.DesktopServices 1.3.4 > /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/ >Versions/A/DesktopServicesPriv >0x925d8000 - 0x92808fff com.apple.Foundation 6.4.7 (567.28) > /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation >0x92914000 - 0x929f2fff libxml2.2.dylib /usr/lib/libxml2.2.dylib >0x92a0f000 - 0x92afcfff libiconv.2.dylib /usr/lib/libiconv.2.dylib >0x92b0c000 - 0x92b23fff libGL.dylib /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Libraries/libGL.dylib >0x92b2e000 - 0x92b86fff libGLU.dylib /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Libraries/libGLU.dylib >0x92b9a000 - 0x92b9afff com.apple.Carbon 10.4 (???) > /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon >0x92b9c000 - 0x92bacfff com.apple.ImageCapture 3.0.4 > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >ImageCapture.framework/Versions/A/ImageCapture >0x92bbb000 - 0x92bc3fff com.apple.speech.recognition.framework 3.6 > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >SpeechRecognition.framework/Versions/A/SpeechRecognition >0x92bc9000 - 0x92bcffff com.apple.securityhi 2.0.1 (24742) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >SecurityHI.framework/Versions/A/SecurityHI >0x92bd5000 - 0x92c66fff com.apple.ink.framework 101.2.1 (71) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >Ink.framework/Versions/A/Ink >0x92c7a000 - 0x92c7efff com.apple.help 1.0.3 (32.1) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >Help.framework/Versions/A/Help >0x92c81000 - 0x92c9ffff com.apple.openscripting 1.2.5 (???) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >OpenScripting.framework/Versions/A/OpenScripting >0x92cb1000 - 0x92cb7fff com.apple.print.framework.Print 5.2 (192.4) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >Print.framework/Versions/A/Print >0x92cbd000 - 0x92d20fff com.apple.htmlrendering 66.1 (1.1.3) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >HTMLRendering.framework/Versions/A/HTMLRendering >0x92d47000 - 0x92d88fff com.apple.NavigationServices 3.4.4 (3.4.3) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >NavigationServices.framework/Versions/A/NavigationServices >0x92daf000 - 0x92dbdfff com.apple.audio.SoundManager 3.9.1 > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >CarbonSound.framework/Versions/A/CarbonSound >0x92dc4000 - 0x92dc9fff com.apple.CommonPanels 1.2.3 (73) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >CommonPanels.framework/Versions/A/CommonPanels >0x92dce000 - 0x930c2fff com.apple.HIToolbox 1.4.8 (???) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >HIToolbox.framework/Versions/A/HIToolbox >0x931c8000 - 0x931d3fff com.apple.opengl 1.4.12 > /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL >0x94096000 - 0x940d0fff libGLImage.dylib /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Libraries/libGLImage.dylib >0x9492b000 - 0x94950fff libssl.0.9.7.dylib > /usr/lib/libssl.0.9.7.dylib >0x96451000 - 0x96451fff com.apple.vecLib 3.3.1 (vecLib 3.3.1) > /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib >0x969cb000 - 0x96a99fff libGLProgrammability.dylib > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/ >libGLProgrammability.dylib >0x96ab4000 - 0x96ab5fff libGLSystem.dylib > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/ >libGLSystem.dylib >0x99756000 - 0x99762fff libXplugin.1.dylib > /usr/lib/libXplugin.1.dylib > >Model: MacPro1,1, BootROM MP11.005C.B01, 4 processors, Dual-Core Intel Xeon, >2.66 GHz, 5 GB >Graphics: NVIDIA Quadro FX 4500, NVIDIA Quadro FX 4500, PCIe, 512 MB >Memory Module: DIMM Riser A/DIMM 1, 512 MB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser A/DIMM 2, 512 MB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser B/DIMM 1, 1 GB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser B/DIMM 2, 1 GB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser A/DIMM 3, 1 GB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser A/DIMM 4, 1 GB, DDR2 FB-DIMM, 667 MHz >Network Service: Built-in Ethernet 1, Ethernet, en0 >PCI Card: NVIDIA Quadro FX 4500, Display, Slot-1 >Serial ATA Device: ST3250824AS P, 232.89 GB >Parallel ATA Device: SONY DVD RW DW-D150A >USB Device: Hub in Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, >500 mA >USB Device: Apple Optical USB Mouse, Primax Electronics, Up to 1.5 Mb/sec, >100 mA >USB Device: Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, 250 mA >FireWire Device: built-in_hub, unknown_value, Unknown > > >___________________________________________________________ >Peter Engelhardt, PhD, docent >Assistant Professor in Molecular Genetics >Unit of Molecular Electron Tomography >Department of Pathology and Virology >Haartman Institute >P.O.Box 21, FIN-00014 Univ. of Helsinki, Finland >Visiting Address: Haartmaninkatu 3, Helsinki >Office Tel: (+358-9)-19126431 (direct) >Laboratory Tel: (+358-9)-19126441 >EM-facilities, Tel: (+358-9)-19126885 >Digiroom: Tel: (+358-9)-1912886 >Fax: (+358-9)-19126491 >FIN-00014 Univ. of Helsinki, Helsinki, Finland > >LCE, Laboratory of Computational Engineering, >Research Center for Computational Science and Engineering >Helsinki University of Technology (HUT), >P.O.Box 9203, FIN-02015 HUT, FINLAND >Visiting Address: Innopolis2, Tekniikantie 14, Espoo > >Home address: > Lindstedstvägen 1 B 7 > FIN-02700 Grankulla, > Finland >Tel: (+358-9)-5091381 > > Mobil Phone: +358 (0)415610171 > Email: Peter.Engelhardt(a)Helsinki.Fi > URL: http://www.lce.hut.fi/~engelhar/ -- ___________________________________________________________ Peter Engelhardt, PhD, docent Assistant Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology and Virology Haartman Institute P.O.Box 21, FI-00014 Univ. of Helsinki, Finland Visiting Address: Haartmaninkatu 3, Helsinki Office Tel: (+358-9)-19126431 (direct) Laboratory Tel: (+358-9)-19126729, 19126442 EM-facilities, Tel: (+358-9)-19126885 Fax: (+358-9)-19126700 Laboratory of Computational Engineering, Research Center for Computational Science and Engineering Helsinki University of Technology (HUT), P.O.Box 9203, FI-02015 HUT, FINLAND Visiting Address: Innopolis2, Tekniikantie 14, Espoo Office Tel: (+358-9)-4514843 (direct) Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: (+358-9)-5091381 Mobile Phone: +358-(0)41 561 0171 Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/

2 1

queries on making image
by bala 09 Nov '06

09 Nov '06

Hello chimera users, 1) I hve to show two molecules in the same figure side by side. When i am displaying, i have a problem that both molecules are not coming at same plane. Is there any option to adjust this. 2) I labelled both these molecules. The labels are coming fine in the screen. But when i create an image (i save it as tif file), some labels are getting hided below my molecular surface. Which option i should use to rectify that. 3) How one can add text on the screen/near a particular spot on the molecule ? 4) Someone kindly Suggest me on best settings (i mean values) of the resolution based on your experience of making figures using chimera or which you normally use. Thanks in advance, Bala

2 1

Re: [Chimera-users] font change in v1.2303+
by Sabuj Pattanayek 07 Nov '06

07 Nov '06

Hi, Yes, now that you mention it I think we have confused each other. I am talking about the fonts in the widgets and dialogs and not the annotation fonts in the linux version. I will grab an old install from http://www.cgl.ucsf.edu/chimera/olddownload.html, and make a screenshot comparing that with the latest 1.2304. I don't think I saw this change in the WinXP version, but I'll check that too. Thanks, Sabuj Elaine Meng wrote: > Hi Sabuj, > It seems like Greg's response was about the labels on the structures, > whereas you said "gui" which I interpret as the widgets and dialogs. > Were you asking about these? I noticed that the font for the "Really > Exit?" dialog is now different, but I haven't seen differences in other > dialogs. > Elaine

2 1

sparky-chimera error
by ksgodin＠u.washington.edu 07 Nov '06

07 Nov '06

Hi all, I having been trying to open an ensemble of NMR structures with the 'km' feature of Sparky. Everything opens fine, but the Model Panel does not open properly. The error log sites Program Files\Sparky\python\lib-tk\Tix.py, line 477, in_init_ self.stylename=self.tk.call ('tixDisplayStyle', itemtype, TclError: invalid command name "tixDisplayStyle" Does anyone know how to fix this? It comes up with Sparky 3.111 and Chimera 1.2065 or 1.1195. Thanks, Kate ~~~~~~~~~~~~~~~~~~~~~~ Kate Godin UW Chemistry Dept Varani Group BAG 63 ~~~~~~~~~~~~~~~~~~~~~~

2 1

font change in v1.2303+
by Sabuj Pattanayek 04 Nov '06

04 Nov '06

Hi, The gui font seems to have changed in v1.2303+ . Is there some way to change it back to the old font? Thanks, Sabuj

2 2

stereo
by hsosa＠aecom.yu.edu 03 Nov '06

03 Nov '06

How can I use stereo (sequential mode) ?. If I click the stereo button in the camera dialog or start chimera using the command chimera --stereo. I get the error message: Unable to turn on stereo viewing Unable to find hardware stereo support (coulddm't choose stereo pixel format Couldn't figure togl widget) My graphic cards is a NVIDIA Quadro4 900 XGL. The Nvdia Stereo driver (v: 91.31) is installed and enabled. Chimera version is: 1 build 2255 2006/06/23 Monitors: Two (dual) digital DELL 1900 FP Computer: Dual Xeon 1.4 Ghz, 1GB of RAM. Running Windows XP Thanks Hernando --

2 4

Showing data set axes
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera supports a format for making geometric objects called BILD described in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Below is a 6 line BILD file that when opened in Chimera shows cylindrical arrows for the X (red), (green), and Z (blue) axes in the style of the program VMD. I made the axes 20 units long, with radius 1 and cone shaped tip with a radius of 2. Tom ----- File axes.bld: .color 1 0 0 .arrow 0 0 0 20 0 0 1 2 .color 0 1 0 .arrow 0 0 0 0 20 0 1 2 .color 0 0 1 .arrow 0 0 0 0 0 20 1 2 > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: Chimera length units > Date: Thu, 2 Nov 2006 17:30:29 -0800 > > i figured some of that but is good to hear it from the source. > > one last question - if i want to make an origin with axes (like a CAD > program might have) so i don't get lost after rotating my volumes a jillion > times and have to click 'orient', is there a way for me to make a > marker-based model (two markers for each axis) and put it slightly > off-origin (like in the -,-,- octant) so that i have a visual on my axes as > i rotate the scene? > > as in, is there a simple way for me to hand-write a marker model that i can > just load and fix to the scene? > > thanks, > > -jeff

1 0

X11 updated for Mac OS X, stereo now?
by David Belnap 02 Nov '06

02 Nov '06

Apple has released an update for X11 with the following comment: This update addresses several issues in the X11 for Mac OS X package, enabling it to better handle: - GLX stereo visuals - offscreen rendering to GLX Pbuffers and Pixmaps I downloaded it and tried to run Chimera (beta version 1 build 2199 2006/01/24) in stereo. It didn't work. Does the X11 update have the stereo-in-a-window capability now that Chimera needs? Is there a newer version of Chimera that will run in stereo on the Mac? David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David_Belnap(a)byu.edu ============================================

2 1

Re: [Chimera-users] Chimera length units
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera clipping and other tools use xyz coordinates and do not use voxel or pixel measures. The volume dialog region bounds panel and the volume dialog step size are exceptions where voxel index positions are used. The notion of a voxel is only relevant to density maps, not atomic models and clippping applies to all kinds of data, not just maps. Screen pixels are a 2 dimensional concept so it is an awkward measure to use especially with perspective 3-d viewing for measuring lengths. Tom > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: Chimera length units > Date: Thu, 2 Nov 2006 14:30:30 -0800 > > does this mean that I can't refer to a given coordinate by pixel/voxel > location without resetting the voxel size to '1 1 1' (which I might not want > to do - does chimera not keep the mrc file (or other voxel data) inside of a > similar kind of array) > > > -----Original Message----- > > From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] > > Sent: Thursday, November 02, 2006 1:46 PM > > Cc: chimera-users(a)cgl.ucsf.edu > > Subject: Chimera length units > > > > > > Hi Jeff, > > > > Chimera does not know what units you are using, the data > > coordinates are just numbers as far as it is concerned. If > > you open a PDB atomic model the coordinates are always > > Angstroms. If you open a density map, say an MRC file, the > > header may include the voxel size. That value could be in > > Angstroms or nanometers. Often maps don't have the true > > voxel size in the header, often they say it is 1. In such > > cases you can use the Chimera volume dialog menu entry > > "Features / Origin and Scale" to set the voxel size in > > Angstroms or nanometers so that the map can be aligned with > > other models or maps. If you open a PDB model in Angstroms > > and a map with the scale set in nanometers then the map will > > look 10 times smaller than it should be relative to the model. > > > > Tom

1 0

Chimera length units
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera does not know what units you are using, the data coordinates are just numbers as far as it is concerned. If you open a PDB atomic model the coordinates are always Angstroms. If you open a density map, say an MRC file, the header may include the voxel size. That value could be in Angstroms or nanometers. Often maps don't have the true voxel size in the header, often they say it is 1. In such cases you can use the Chimera volume dialog menu entry "Features / Origin and Scale" to set the voxel size in Angstroms or nanometers so that the map can be aligned with other models or maps. If you open a PDB model in Angstroms and a map with the scale set in nanometers then the map will look 10 times smaller than it should be relative to the model. Tom > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Date: Thu, 2 Nov 2006 13:26:11 -0800 > > thanks Tom, > > sorry for a goofy question, but how do I know what units chimera is using > (for measuring distances, having the output is nice in Angstroms, but > sometimes (like with orienting a clipping plane) using unitless/pixels is > more handy for displacements/etc) > > thanks, > > -jeff

1 0

Per-model clipping plane command
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, There isn't yet a Chimera command for per-model clipping. Below is some Python code that can do it. Open a density map and then open this Python code in Chimera to clip it. Some more code can make it loop through different depths. There is some trickiness to making it update the graphics window in such a loop. Ask for details if you want that. Tom > From: Jeff > To: <goddard(a)cgl.ucsf.edu> > Subject: per-model clipping plane question (or similar) > Date: Thu, 2 Nov 2006 10:54:26 -0800 > > hi Tom, > > was wondering if I can control the per-model clipping plane > orientation/parameters/etc via command line or shortcuts - > > would like to be able to methodically push a clipping plane in 'slab mode' > through my model to compare it w/ other 2D/projection tools I use - I know I > can click 'orient' on the model and it will orient to a default > position/rotation (and I can click orient on the per-model clipping plane > and therefore register them both), but is there then a way that I can > specify (say, along one axis, like z) where the slab/clipping plane is > positioned, like in pixels? > > can I control the angular position of the clipping plane via command line, > too? > > thanks, > > Jeff ----- Python code clip.py. # ----------------------------------------------------------------------------- # Python function to control per-model clipping (like menu entry # Tools / Depiction / Per-Model Clipping). The clip plane rotates with # the model (PDB structure, density map, ...). # # Parameters: # model is a Chimera Model # origin is (x,y,z) of point on clip plane. # normal is (nx,ny,nz) pointing towards clipped (invisible) half of plane. # slab_thickness is in data length units (usually Angstroms). # # Origin and normal are relative to the data coordinate system, for example, # the x,y,z coordinates of a PDB atoms or axes of a density map. The clip # def set_clipping(model, origin, normal, slab_thickness = None): p = model.clipPlane from chimera import Point, Vector p.origin = Point(*origin) p.normal = Vector(*normal) model.clipPlane = p model.useClipPlane = True if slab_thickness == None: model.useClipThickness = False else: model.clipThickness = slab_thickness model.useClipThickness = True # ----------------------------------------------------------------------------- # Cap holes left when clipping a surface. Controls graphical interface # shown by menu entry Tools / Depiction / Surface Capping. # # Parameters: # cap_color is (r,g,b) or (r,g,b,a) where values in range 0-1 # cap_mesh is True or False for mesh or solid cap appearance # cap_subdivision of 2 makes cap mesh twice as fine for detailed coloring. # cap_offset in data length units (usually Angstroms) for large models # sometimes needs to be larger to avoid cap itself being clipped due to # finite floating point precision in OpenGL. # def show_surface_caps(show, cap_color = None, cap_mesh = False, cap_subdivision = 1, cap_offset = 0.001): from SurfaceCap.gui import capper_dialog d = capper_dialog(create = True) d.Close() use_color = (cap_color != None) if use_color: d.use_cap_color.set(use_color) d.cap_color.showColor(cap_color) if cap_mesh: d.cap_style.set('mesh') else: d.cap_style.set('solid') d.subdivision_factor.set(cap_subdivision) d.cap_offset.set(cap_offset) d.show_caps.set(show) # ----------------------------------------------------------------------------- # Example using set_clipping(). # from chimera import openModels mlist = openModels.list() m = mlist[0] set_clipping(m, (.5,0,1), (0,1,1), 8) show_surface_caps(True, (1,0,0), True) # Red mesh caps

1 0

Chimera under FreeBSD
by Devon Ryan 01 Nov '06

01 Nov '06

Has anyone had success getting chimera to run under FreeBSD? I can get the linux version to start (under the linuxulator), but it crashes after ~20 seconds when the bundled version of python core dumps. I'm running FreeBSD 6.1 on an intel architecture. Thanks -- Devon Ryan | dpryan(a)sg.uchicago.edu Neuro Grad Student, Ptacek Lab | dpryan(a)phy.ucsf.edu University of Chicago '02 | dpryan(a)alumni.uchicago.edu www.dpryan.com | dpryan(a)dpryan.com ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

3 2

question regarding chimera 1.2304-wim32.exe
by AJ Campbell 31 Oct '06

31 Oct '06

I have tried installing Chimera several times on my Windows machine but keep receiving an error message saying "Outline highlight not supported by hardware", any advice would be appreciated. ~ Arthur

3 3

atom name balloons
by Greg Pintilie 31 Oct '06

31 Oct '06

I was wondering why in the new release of Chimera ballons no longer pop up when the mouse is placed over an atom and is left there... is this an option that has to be set somewhere? I found it extremely usefull and now am missing it... Greg

2 1

problems with starting Chimera
by Mareike Goeritz 30 Oct '06

30 Oct '06

Hello, I'm interested in using Chimera, but after downloading and installing the software I'm unable to launch the program. I always get the following error message: "Microsoft Visual C++ Runtime Library: Assertion failed! Program: C:\Program Files\Chimera\bin\pythonw.exe File: togl.c Line: 2994 Expression: res==TRUE For information on how your program can cause an assertion failure, see the Visual C++ documentation on asserts (Press Retry to debug the application - JIT must be enabled)" I'm not familiar with C++, so I don't know what to do. Does anybody know what might be missing or what's the problem? Thank you for your help!! Mareike -- ******************************** Dr. Mareike Goeritz Department of Chemistry, MC 164-30 California Institute of Technology 1200 E. California Blvd. Pasadena, CA 91125 (626) 395-6032 Tel (626) 683-8753 Fax goeritz(a)caltech.edu ********************************

2 1

Chimera, 3dsmax, blender
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Lydia, It's been years since I've had access to a 3dsmax license, so I can't really make good comparisons between it and Blender. Fundamentally, they serve the same role, so I expect you would find using them similar, especially compared to PyMOL, Chimera, etc. Before getting into the benefits, you should be aware that compared to any software truly designed for chemical modeling, Blender has some serious drawbacks. There is no pre-existing set of structural tools that is standard for chemistry modeling software: if you want ribbons, you have to write a procedure that will generate them. I'm assuming you're already familiar with this, though, since you're using 3dsmax. As another sizeable negative, CSG in Blender is still somewhat flaky. I seem to remember having far fewer problems in 3d studio, even back around ~R5 or 6. On the benefit side, Blender's plugin/scripting system is extremely free of restrictions. The scripting system is pure Python, and many Python "plugins" are available. The true plugins are done in C, but are currently restricted to some post-processing features. You could also use the scripting system to access C libraries. These features really help to make up for the lack of built-in chemistry-centered tools. The other reason why you might prefer Blender over 3dsmax is that the scripting and plugin system is very much like Chimera, so if you're using both it's only one system to learn. Jonathan > Message: 8 > Date: Mon, 30 Oct 2006 14:47:06 -0800 > From: "Lydia Jablonski" <lydka(a)uoregon.edu> > Subject: [Chimera-users] Exporting VRML, Using Blender > > Jonathan and Greg- > > Thank you for your suggestions. I wanted to at least try them before I responded. > > Exporting VRML: I did try the export to VRML from version 1.2304 and it is good to know that it works for ribbons now. Unfortunately, the imported VRML meshes don't seem to respond to the mesh smoothing in 3ds max. With the .pdb --> .pov --> .3ds --> .max workflow I'm able to get a completely smooth surface on the ribbon. With the imported .wrl (VRML) I am able to see the triangulation on the surface, especially with shiny materials. Increasing the subdivision quality in Chimera makes these triangles smaller, but they are still visible. > > Blender: Can you explain more the advantages of Blender for rendering/animating molecular models? I've been using 3ds max for quite a while (since the DOS days) so I feel very comfortable with it. But the need to work with molecular models is new so I'm still bumping around trying to figure out what all the possibilities are. If another 3D animation program would work better with exported .pdb files I'd be willing to pick it up. > > Any more pointers would be much appreciated. > > -Lydia

1 0

Toolbar and Favorite on PC
by jean-francois menetret 30 Oct '06

30 Oct '06

Hello all, when running chimera on my PC (windows XP), my toolbar stopped being displayed. If I uninstall and reinstall chimera, my toolbar comes back until the next reboot. How can I fix that ? Is there to restore my preferences after launching chimera? Regards Jean-Francois Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

2 4

Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 19
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although this does not relate to your question on licensing, is there any particular reason you're using such a complicated workflow? Chimera can be used to generate basic geometry (sphere/cylinder) from PDB files via povray, but so could any import system you have for the 3D modeling software. You would also lose the benefit of chemistry-centered structure for manipulation or selection: chains, residues, etc. I've been using Blender to handle complicated chemical models for a while now, and it wasn't that difficult to implement the import of various data types. With BioPython pdb files become trivial, and volumetric data sets are (very) difficult but possible. Jonathan > Hello- > > Do any of you have an idea of how much a single commercial license for Chimera would cost? > > I'm a 3D artist/animator/biology student that works at in the art dept. of a biotech company. I'm interested in the exporting .pdb files to .pov, then converting to .3ds to import to 3ds max. > > Thanks, > > Lydia Jablonski

3 3

changing center of rotation
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although I haven't used EMAnimator, you can set the center of rotation within Chimera using the Set Pivot action: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot There's also Tools/Movement/Rotation, and lastly, you can edit structures to insert artificial points at extreme high/low XYZ locations, which will in effect manually set the center used via the 'center of models' option. I wouldn't recommend the last option unless you have a good reason to do so, but it does work. Jonathan > Message: 1 > Date: Mon, 30 Oct 2006 11:52:42 -0800 (PST) > From: wendy ochoa <wencryo(a)yahoo.com> > Subject: [Chimera-users] rotating molecules for movies > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <20061030195242.57847.qmail(a)web37306.mail.mud.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? > Thanks > > > >

1 0

Re: [Chimera-users] viewing grid density
by Thomas Goddard 30 Oct '06

30 Oct '06

Bala reports that the problem was in an Amber input file. > From: "bala" <bala(a)igib.res.in> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] viewing grid density > Date: Fri, 27 Oct 2006 19:59:38 +0530 > > Hello Thomas and Elaine, > > Thank you for your information. I rechecked the amber input files and i = > found a mistake there in rms fitting the coordinates in my trajectory. > > regards, > Bala

1 0

Re: [Chimera-users] rotating molecules for movies
by Thomas Goddard 30 Oct '06

30 Oct '06

Hi Wendy, Here are some Chimera commands that are useful for making movies with Movie Recorder: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/moviecomm… Here's a fancier Chimera movie script example. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/1gfl.com Here is the documentation for the Movie Recorder dialog and movie command: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html Tom

1 0

rotating molecules for movies
by wendy ochoa 30 Oct '06

30 Oct '06

Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? Thanks

2 1

generating electrostatic potential map
by bala 27 Oct '06

27 Oct '06

Hello all, I want to generate the electrostatic potential map using Chimera. I tried through Delphi controler, however i am repeatedly getting an error as follows. I have successfully installed Delphi. Can someone suggest me what is wrong. __________DelPhi V. 4 Release 1.1 ______________ | | | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | many dielectric regions, multisalt ionic | | strength, different probe radii, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | | Recompiled on Linux and PC | | January 2002 -------- Walter Rocchia | |__________________ ___________________| DelPhi V. 4 program started on Fri Oct 27 2006 at 14:55:00 opening parameter file /tmp/tmpvpgS8V At least 30 nonlinear iterations atom radii read from file /usr/people/ojha/BALA/chim_amber.siz unknown header format in radius file: O5' A 1 1.7210 First it showed the same for H5 atom [which was the first atom in the siz/charge file], then i just tried by deleting the first line in the radius and charge file. Then the same error is coming for the second atom O5' in the file. Thanks in advance, Bala

2 1

viewing grid density
by bala 26 Oct '06

26 Oct '06

Hello all, 1) I hve generated a solvent density map using Amber8 in XPLOR format. I am able to open the map in chimera. I hv also generated a refernce pdb file. Now i have to fix the reference structure of my molecule in the density map. I tried many options but i couldnt do that. Someone pls suggest me how i should do the same. 2) Also i am not clear with the meaning of the threshold levels given in the histogram. Although i could see the difference in the density map by sliding the vertical bar to various postions, i am getting what it can tell us exactly. Which is the most suitable threhold level etc. 3) Someone pls give me the link for the chimera mail list archive...i am unable to locate it. Bala

3 2

To except box information in MD movie
by Atsutoshi Okabe 25 Oct '06

25 Oct '06

Hello, I viewed Amber format trajectory files ( topology/parameter file and trajectory file ) by MD movie. But I got the figure( attached file) I didn't intend. I think the reason is to read box information in the Amber trajectory file . How can I except the box information in MD movie window ?

2 1

To color atoms
by Atsutoshi Okabe 24 Oct '06

24 Oct '06

Hi, I visualized one ligand molecule (a kind of sugar) written by PDB format within chimera. But all atoms have non color(attached file ) I want to color these atoms (i.e. the oxygen has red .) Could you please teach me how to color atoms?

2 1

1.2304 production
by Eric Pettersen 23 Oct '06

23 Oct '06

We haven't received any major bug reports for the release candidate, so we have promoted it to a production release (1.2304) which includes a few quite minor bug fixes and some documentation improvements relative to the release candidate. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

Movie - Display Spheres
by Jared Godar 20 Oct '06

20 Oct '06

Hello, I am trying to use the 'represent spheres' command to draw attention to specific residues in a model that is displayed as a ribbon. I would like to first show the ATP binding site of the molecule with magenta spheres, then show the three residuse which get phosphorolated. Currently, I am able to display one of these elements or the other as spheres, but not both at the same time. I've tried to use a single represent sphere command to specify all of the desired atoms, but can't seem to get the context right, represent sphere #0:426,431,432,ATP and represent sphere #0:426,431,432 & #0::ATP weren't working. Help on the syntax to simultaneously display the two commands listed below which are currently mutually exclusive would be appreciated. #SHOW ATP: color magenta #0::ATP; color magenta #0::mg; represent sphere #0::ATP #SHOW PO4 Residues show #0:426,431,432; color yellow #0:426; color orange red #0:431; color red #0:432; represent sphere #0:426,431,432 Thanks, Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Department of Molecular Physiology & Biophysics 708 Light Hall 2215 Garland Ave. Nashville, TN 37232-0615 Work: 615.322.7898 Fax: 615.322.7236 jared.godar(a)vanderbilt.edu

2 1

Dock?
by S Joshua Swamidass 19 Oct '06

19 Oct '06

Hello, Are there any plans to develop a gui frontend for DOCK using chimera? Josh

4 3

force fitting a protein into select volume in a EM reconstruction
by jayant_jacques 17 Oct '06

17 Oct '06

hi! Is it possible in chimera to choose a particular part of a EM envelope and a protein and fit them? AS the protein that I am trying to fit into the map finds a better fit else where in the EM envelope, after I painstakingly align it to the place where its supposed to be!!! Thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

2 1

release candidate
by Eric Pettersen 17 Oct '06

17 Oct '06

We've made a release candidate (version 1.2303) available for download. It has many new features relative to the previous production release (1.2199). The features/improvements are listed here: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2303.html Please let us know if you encounter any problems with the release candidate. If no major problems surface in the next few days, we will promote the candidate to production release status. Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

viewing
by jayant_jacques 17 Oct '06

17 Oct '06

Hi! I thank chimera users for answering and helping me in fitting my protein into EM Map. I have a small problem. When I rotate the protein, portions of the map and protein come into view and dissappear. I am not able to figure out how to turn off this feature in chimera! I would be grateful if told how to turn off this feature. Thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

3 2

Re: [Chimera-users] About Chimera under Linux64
by Thomas Goddard 17 Oct '06

17 Oct '06

Hi Quentin, I suggest you use the 32-bit Linux Chimera version 1.2255. Or if you wait a few days a new 32-bit Linux Chimera version 1.2303 will be coming out. We do not regularly build a 64-bit Linux Chimera because we do not have a 64-bit Linux system in our lab. (I'll have to check on this -- maybe we have one now.) The only 64-bit version we routinely distribute is for the very obscure Tru64 operating system running on computers with Alpha processors. The current 64-bit Linux build (May 2005) is so old that it lacks many useful features for looking at EM maps. The reason we have not moved more quickly to support 64-bit distributions is because Chimera is strongly oriented towards interactive calculations -- that is calculations taking at most a few seconds. On gigabyte size data there is almost nothing that can be done in a few seconds. Still we understand that you may look at the data subsampled (using the volume dialog step size) and then want to create an image at full resolution (for example for a publication or talk) that may take many minutes to render and will need alot of memory -- not easily accomodated in a 32-bit address space. It is our plan to regularly distribute 64-bit Linux and Windows version in the future -- probably within a year. The main hold-up is that we do not have 64-bit machines setup in our lab yet. The usual method of working with large EM tomograms in Chimera is to focus on smaller regions of interest so that segmentation can be done interactively. Practical size chunks of data are 256^3. You can select these smaller regions in Chimera. For large pieces the graphics hardware is not able to render fast enough to allow smooth interactive rotation used in segmenting interactively. It is possible to display larger volumes and just display every other data plane along each axis. Tom > Date: Tue, 17 Oct 2006 14:11:12 +0200 > From: Quentin <derobill(a)mpi-cbg.de> > User-Agent: Thunderbird 1.5.0.7 (X11/20060922) > To: goddard(a)cgl.ucsf.edu > Subject: About Chimera under Linux64 > > Dear Mr. Goddard, > > I have been setting up the EM tomography in the Max-Planck Institute for > Molecular Cell Biology and Genetics Dresden (www.mpi-cbg.de Germany ) > since one year. We have a tecnai F30 dedicated for tomogram acquisition > and it runs after some efforts, with SerialEM/IMOD. I would like to > improve now the segmentation part of our work which is the bottleneck in > our fields. So I strive now to get a good set of software to segment and > visual our huge(600Mb to 6Gb) 3d electron density map (.mrc file format). > > Manfred Auer and Sergio Marco oriented me on your work, i.e. the volume > data display tools in Chimera. The first tests I did the last days, look > really promising. Your work is really helpful for the 3D Electron > Microscopy community. Thanks. > > I am just wondering why the compiled version for Linux64 of Chimera is > so old(May 17,2005). Is there some reason? Should I use a newer 32bit > version ? typically our dataset are 600Mb to 5Gb and we are running a > dual core Athlon 64 machine with soon 8Gb memory under Ubuntu64bit. > > Thanks for your attention, > > Best regards, > > Quentin de Robillard > > Pfottenhauerstr. 108 > 01307 Dresden > +49 351 210 20 61 >

1 0

Re: [Chimera-users] fitting a protein inside an EM reconstruction
by Elaine Meng 12 Oct '06

12 Oct '06

Hi Jayant, Selecting something is not the same as making it movable. Selecting something makes Actions menu items apply to it. If you want to make different models movable/unmovable, use the "Active" checkboxes in the Model Panel (Favorites... Model Panel), or various "activate" functions in the right side of the Model Panel, or the small checkboxes under the Command Line (Favorites... Command Line). These activation methods determine which models can be moved with the mouse or with movement commands like "move" and "turn." As Tom said, however, the fitting tool requires atoms to be selected. Even if only a few atoms are selected, the fitting will move the entire model containing the atoms, but maximize the density values at the selected atoms. I hope this helps, Elaine On Oct 12, 2006, at 10:14 AM, jayant_jacques wrote: > > Hi! > I have been trying to fit a protein into an EM reconstruction. > > methodology > I display my protein of interest and EM map on the same window. > I select the protein and if I click fit. > > Problem > 1. Nothing happens!! If I move the protein the whole frame moves as a > whole. > 2. Also is it possible to click drag the protein into the envelope > and then give the fit command such that the program will take over the > fitting. As I have 3 proteins to fit into this EM Map. > > Thanks > Jayant > Jayasundar Jayant James > Postdoc, > Department of Veterinary and Comparative Anatomy, Pharmacology > and Physiology(VCAPP), Washington state university, Pullman > 99164-6520, USA. > http://www.chick.com/reading/tracts/0001/0001_01.asp > Phone office:335-5937, Cell:1-509-432-5790 > > <1963059423(a)Middle5.gif> ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

fitting a protein inside an EM reconstruction
by jayant_jacques 12 Oct '06

12 Oct '06

Hi! I have been trying to fit a protein into an EM reconstruction. methodology I display my protein of interest and EM map on the same window. I select the protein and if I click fit. Problem 1. Nothing happens!! If I move the protein the whole frame moves as a whole. 2. Also is it possible to click drag the protein into the envelope and then give the fit command such that the program will take over the fitting. As I have 3 proteins to fit into this EM Map. Thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

2 1

Fwd: single-sequence FASTA file does not open
by Lucas J. Thode 12 Oct '06

12 Oct '06

Oops, sorry about double-posting this, but I forgot to mention that I am not on the list, so remember to CC me. ----- Original Message ----- In Chimera beta 1 build 2199 on Windows XP Professional SP2, I cannot open a FASTA file that contains a single sequence. (The file in question is attached and looks to be a valid FASTA file according to the documentation I have read on the FASTA format.) What should I do about this issue? Error log: Opening F:\H Biotech Engineering\cftr.fasta Error reading F:\H Biotech Engineering\cftr.fasta: IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech Engineering\cftr.fasta'; check your alignment file for errors (see reply log for Python traceback info) Traceback (most recent call last): File "C:\Program Files\Chimera\share\__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in init tkgui.eventLoop() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757, in eventLoop app.mainloop() File "C:\Program Files\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "C:\Program Files\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 229, in <lambda> self.__buttonFuncName(txt))() File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 470, in OK self.Apply() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 160, in Apply openPath(path, ftype) File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 258, in openPath mols = chimera.openModels.open(path, type=ftype) File "C:\Program Files\Chimera\share\chimera\__init__.py", line 1086, in open models = func(filename, *args, **kw) File "C:\Program Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 33, in <lambda> lambda fn, e=emo, ft=fileType: e.open(fn, ft), File "C:\Program Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 25, in open self.module('MAViewer').MAViewer(fileName, fileType) File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line 59, in __init__ seqs, fileAttrs, fileMarkups = self.readFile( File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line 761, in readFile seqs, fileAttrs, fileMarkups = parseFile(fileName, fileType) File "C:\Program Files\Chimera\share\MultAlignViewer\parse.py", line 100, in parseFile raise IOError("Only one sequence found in %s file" IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech Engineering\cftr.fasta'; check your alignment file for errors Done opening F:\H Biotech Engineering\cftr.fasta

3 2

single-sequence FASTA file does not open
by Lucas J. Thode 12 Oct '06

12 Oct '06

In Chimera beta 1 build 2199 on Windows XP Professional SP2, I cannot open a FASTA file that contains a single sequence. (The file in question is attached and looks to be a valid FASTA file according to the documentation I have read on the FASTA format.) What should I do about this issue? Error log: Opening F:\H Biotech Engineering\cftr.fasta Error reading F:\H Biotech Engineering\cftr.fasta: IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech Engineering\cftr.fasta'; check your alignment file for errors (see reply log for Python traceback info) Traceback (most recent call last): File "C:\Program Files\Chimera\share\__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in init tkgui.eventLoop() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757, in eventLoop app.mainloop() File "C:\Program Files\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "C:\Program Files\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 229, in <lambda> self.__buttonFuncName(txt))() File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 470, in OK self.Apply() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 160, in Apply openPath(path, ftype) File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 258, in openPath mols = chimera.openModels.open(path, type=ftype) File "C:\Program Files\Chimera\share\chimera\__init__.py", line 1086, in open models = func(filename, *args, **kw) File "C:\Program Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 33, in <lambda> lambda fn, e=emo, ft=fileType: e.open(fn, ft), File "C:\Program Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 25, in open self.module('MAViewer').MAViewer(fileName, fileType) File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line 59, in __init__ seqs, fileAttrs, fileMarkups = self.readFile( File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line 761, in readFile seqs, fileAttrs, fileMarkups = parseFile(fileName, fileType) File "C:\Program Files\Chimera\share\MultAlignViewer\parse.py", line 100, in parseFile raise IOError("Only one sequence found in %s file" IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech Engineering\cftr.fasta'; check your alignment file for errors Done opening F:\H Biotech Engineering\cftr.fasta

1 0

Vilualizing solvent distribution
by Atsutoshi Okabe 11 Oct '06

11 Oct '06

Dear all, I want to visualize solvent(water) distributions around one solute molecule. I do molecular dynamics calculation with Amber8 program. So I got the following ouput file using grid command of Ptraj module to analyze trajectories. This line is ignored 1 rdparm generated grid density 100 -49 50 100 -49 50 100 -49 50 30.000 30.000 30.000 90.000 90.000 90.000 ZYX -49 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 I think the output is in the format of a XPLOR formatted contour file and can visualize this output data within chimera soft ware. But I don't know how to treat this out put file in chimera . Can I use this file directory in chimera or have to do anything else before I use chimera? Thanks Atsutoshi

2 1

Request: can model selection be added to the pull down selection menu?
by Boaz Shaanan 10 Oct '06

10 Oct '06

Hi, I wonder if you could consider adding the option of selecting models to the pull-down selection menu. Right now, only chains (and other things) can be selected but quite often, when reading different models with the same chain names, the only way to select specific chains from a model would be by using the command line where models can be specified. This works of course, but having the model-selection option in the pull-down menu might add flexibility. What do you think ? Regards, Boaz Boaz Shaanan, Ph.D. Associate Professor Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel‎

3 2

Re: [Chimera-users] window size
by Viktor Hornak 06 Oct '06

06 Oct '06

Hi Elaine, this is exactly what I needed. Also, thanks for a pointer to experimental features page (it's nice!). One other vaguely related question I had was whether it's possible to find out what chimera commands correspond to actions picked from menus or panels (e.g. Actions->Atoms/Bonds->Hide; Camera -> orthographic from Viewing/Side View panel, etc.). My objective is to capture everything I do in a specific session in chimera command scripts, which have an advantage over saving the session in that 1) I see what I did directly in the script, 2) these scripts are much smaller than session files. Thanks for your help! -Viktor Elaine Meng wrote: > Hi Viktor, > From our experimental features page > > http://www.cgl.ucsf.edu/chimera/experimental/experimental.html > > you can download a "set magnification and window size" feature that > includes a "windowsize" command. > > A related feature (unfortunately broken in past releases, but will be > available in the next release) is the --geometry startup option. We > plan to make a release this month. The --geometry option is not quite > as straightforward as the windowsize command, because depending on the > system, the specified size might include some of the bars around the > graphics window. However, that just means you need to try it once, > use the "get pixels" button on the image-saving panel (File... Save > Image) to determine the actual graphics window dimensions, and at the > next startup use --geometry with the necessary additions or > subtractions to achieve the target size. That's what I've been doing. > > Startup options are described here: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html > > However, if you are on a Windows system, it is not very convenient to > use startup options (one way is to make a separate Chimera shortcut > and modify its properties). If you are on Windows, getting the > "windowsize" command from the experimental features page may be the > way to go. > > I hope this helps, > Elaine > > On Oct 6, 2006, at 5:43 AM, Viktor Hornak wrote: > >> Dear All, >> >> I was wondering if there's chimera command that sets the size of chimera >> window. Basically I just want to have a well defined window size when I >> save pictures (or movies)... >> >> Thanks, >> -Viktor >> >> -- >> Viktor Hornak >> SUNY at Stony Brook >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html

2 1

fitting a protein inside an EM reconstruction
by jayant_jacques 06 Oct '06

06 Oct '06

hi! I am having a small problem in fitting crystal structures into the EM reconstruction. Problem definition When I open the protein that I am trying to fit into the EM map along side the EM map, the Em Map shrinks. The EM map which is the super set, which holds 3 proteins appears shrunk with respect to the protein that I am trying to fit inside the EM Map and the crystal structure How am I to overcome this hurdle? thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

2 1

window size
by Viktor Hornak 06 Oct '06

06 Oct '06

Dear All, I was wondering if there's chimera command that sets the size of chimera window. Basically I just want to have a well defined window size when I save pictures (or movies)... Thanks, -Viktor -- Viktor Hornak SUNY at Stony Brook

2 1

OpenGL error in GfxInfo::initialize 'out of memory'
by Dmitry Osolodkin 05 Oct '06

05 Oct '06

Hello all, I have a very small but annoying problem. I had two versions of libGL.so.1, so I have renamed the version in /usr/X11R6/lib/. Now I can run Chimera, but it works rather slow and says OpenGL error in GfxInfo::initialize 'out of memory'. I use Mandriva Linux 2006 and FireGL drivers by ATI. Could anone help me? Thanks. Dmitry Osolodkin

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 2
by Jonathan Hilmer 05 Oct '06

05 Oct '06

Pu Qian, Although resources-intensive, I find it useful to have multiple, identical, overlapping copies of the same density set. It allows complex 'removal' of sections in the final image by the combination of multiple clipping planes. For example, the three planes with definitions of [1,0,0], [0,1,0], and [0,0,1] all with an origin at the center of your data will cut away 1/8 of a spherical region, if you have three copies of the density loaded. This also makes it easy to animate the cutout. The alternative is to use the volume eraser (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/volerase…) which works, but I've found it less useful for movies. When working with large data sets and this method, use cropped density sets to minimize unnecessary resource usage. Jonathan > > To whom it may concern, > > > > I'm a new user of Chimera. It is a very good software! > > > > Here, I would like to ask you a few questions? To show inside of > > protein > > (3d model),I need to cut it into half (sometime, maybe only part, > > for example, > > 1/4 etc.). Just like an apple, if I want to show its core, I need > > to cut the > > apple into two parts from its middle. Does Chimera has such > > function? (I think > > it has.) My 3d data comes from electron microscopy single particle > > analysis > > using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so, > > which type of > > 3d data I should produce for Chimera? It would be a great > > appreciated if you > > could reply me in your convenience. Hope it will not bother you too > > much. > > > > Sincerely yours, > > > > > > Pu Qian > > > > Dr. Pu Qian > > Department of Molecular Biology > > The University of Sheffield > > Firth Court, Western Bank > > Sheffield, S10 2TN > > UK

1 0

Spider to Brix
by Batsal Devkota 05 Oct '06

05 Oct '06

Hi, When I convert spider file to brix and load both of them in Chimera, they do not superimpose on top of each other. I adjusted the origin to be 0,0,0 for both the maps and still the maps seem to be rotated with respect to one another. any insight?? Thank you, Batsal. -------------------------------------------------- Batsal Devkota Graduate Student, School of Biology GeorgiaInstitute ofTechnology Atlanta, GA 30332-0400

2 1

volumetric filling
by jayant_jacques 04 Oct '06

04 Oct '06

hi! I am striving to perform voluertric filling of a crystal structure into an EM reconstruction. I have down loaded and complited the Linux_64 bit version. I first load my crystal structure and then the EM reconstruction on the same screen and set the EM reconstruction as DATa. I am not able to figure out where the FIT buttons is located in the pop up menus!!! I would be very grateful if you could help me sort out this issue! Thanks Jayant NB I am using the online manual to help me in this endeavour http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodel… Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

4 3

Slicing a 3d model
by Thomas Goddard 04 Oct '06

04 Oct '06

Hi Pu Qian, Use clip planes to cut a model in half in Chimera. There are two types of clip planes. The front and back clip planes are always parallel to the screen. The per-model clip planes can be oriented at any angle. Both can clip away the back as well as the front. The following web page describes how to use both for EM density maps. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#slab Clipping works on all types of data in Chimera including atomic models of proteins. For EM data it helps to have Chimera cover the holes left when a contour surface is clipped. This is described here. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#capping Also you can color according to density on the sliced surface. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorc… All of these URLs come from the Chimera guide to volume display http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html and you may find other useful features for viewing your EM map there. The following page shows examples of clipping, capping and coloring including a movie of a slab moving through an EM map of a virus particle. http://www.cgl.ucsf.edu/chimera/experimental/viper_em/viper_em.html Chimera reads many density map file formats (CCP4, MRC, SPIDER, O, XPLOR, Purdue image format, ...) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume I do not know if IMAGIC5 uses any of these formats or has its own. Chimera does not read any specific IMAGIC5 format. Tom > From: P Qian <P.Qian(a)sheffield.ac.uk> > Date: October 4, 2006 1:43:50 PM PDT > Subject: Sheffield Qian, how to make cut 3d model > > > > To whom it may concern, > > I'm a new user of Chimera. It is a very good software! > > Here, I would like to ask you a few questions? To show inside of > protein > (3d model),I need to cut it into half (sometime, maybe only part, > for example, > 1/4 etc.). Just like an apple, if I want to show its core, I need > to cut the > apple into two parts from its middle. Does Chimera has such > function? (I think > it has.) My 3d data comes from electron microscopy single particle > analysis > using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so, > which type of > 3d data I should produce for Chimera? It would be a great > appreciated if you > could reply me in your convenience. Hope it will not bother you too > much. > > Sincerely yours, > > > Pu Qian > > Dr. Pu Qian > Department of Molecular Biology > The University of Sheffield > Firth Court, Western Bank > Sheffield, S10 2TN > UK >

1 0

Re: [Chimera-users] Merge PDB Question
by Jonathan Hilmer 28 Sep '06

28 Sep '06

On the issue of using Chimera to write PDB files, would it be possible to change the format of the PDB output Chimera generates? I'm not too well-versed in the details of the pdb file format, but I ran into issues using Chimera-generated structures with a Blender plugin that used BioPython to handle parsing the files. Although I can't remember the details off the top of my head, it involved the use of multiple 'END' statements to separate models (in Chimera-generated files). It was easy enough to write a script to substitute 'MODEL', 'ENDMDL' pairs, but I'm sure it would be better implemented in whatever library handles the file IO in Chimera. Jonathan > Date: Thu, 28 Sep 2006 10:38:00 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Merge PDB Question > To: "Jared Godar" <jared.godar(a)vanderbilt.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <4F99156D-A681-4EFB-AC6C-5A0C57D029E0(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Jared, > Currently you cannot bond different models, and the only way to > "merge" is to put the atoms in the same file before opening it. > There are actually other reasons your command wouldn't work: > > - seems to me that there is no model 1, only 1.1, 1.2, 1.3 and 1.4, > so the first part would specify zero atoms > - the ampersand & stands for intersection (logical AND, not english > and) and should be omitted, e.g. > command: bond #1.1:504.b@c #1.1:505.b@n > > What I've done in the past to handle similar cases (splicing stuff > from an NMR structure onto a Xray structure) is to first put the tail > (with a few extra residues to overlap with residues that are already > present) into a file by itself. Then I open that new file, so it > will be a new, separate model. I then match that model onto the > original model using atoms in the overlapping part. Then, write out > another PDB file of the tail relative to the untransformed original > model. Using text-editing, remove the part that overlaps since it > was just there for positioning purposes. FINALLY (text-editing > again) make another PDB file that combines the new tail with the > original protein. They may need to have the same chain ID as well. > Sorry this is such a long process. If you think you can hand- > position the tail sufficiently well you could skip the parts about > having the extra atoms, using them for matching, and deleting them. > > If you remove any intervening TER, the bond will already be there > when you open the new file. > > I hope this helps, > Elaine

2 1

Re: [Chimera-users] [chimera-dev] chimera help
by Eric Pettersen 28 Sep '06

28 Sep '06

If you have a large number of PDBs then you might want to use Python, where you have access to loops and variables. Say you had the PDBs listed in a file, one per line, named "mypdbs". Then you might use a Python script like this: -------------------------------------- import chimera from chimera import runCommand f = open("mypdbs", "r") for line in f: pdbID = line.strip() runCommand("open " + pdbID) runCommand("scale 1.5; ~disp; ribbon; ribrepr smooth; rainbow") runCommand("copy file %s.png png supersample 5" % pdbID) runCommand("close all") -------------------------------------- Note that the "runCommand" function allows you to do things that you know the Chimera command for without knowing what the Python equivalent is. Assuming you name the script file with a ".py" ending so that Chimera can recognize it as Python, then you can run the script with any of the ways that Chimera opens files (File...Open dialog, "open" command, startup shell command argument). Also, Chimera needs the graphics window to be showing and not obscured by other windows in order to render the images. If you are doing a lot of images you may have to turn off your screen saver so that it doesn't hide the Chimera window. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On Sep 28, 2006, at 9:14 AM, Elaine Meng wrote: > Hi Vishal, > Actually you can do this with a Chimera command script, as opposed > to programming in Python. A command script just contains the same > commands you would enter in the Command Line. I'm not sure of what > type of saving you had in mind, " but the "copy" command can be > used to save an image file, "save" to save a session, and "write" > to save a PDB file. > > This page links to all the command man pages, plus it discusses > command scripts (at the bottom): > http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/ > framecommand.html > > Just opening the command file will execute the commands. > Here are links to a couple of example command files: > http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/tutorials/ > setup.com > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/ > 1gfl.com > > And here is another, between the dashed lines: > ----------------------------------------------------------------- > open 1hxx > open 1pho > modelcolor coral #0 > modelcolor cornflower blue #1 > ~disp; rep bs; ribbon; ribrepr smooth > matchmaker #0 #1 > ----------------------------------------------------------------- > > I guess the main difficulty if you are saving images is how to get > a good view of the structures. Usually some rotation, scaling, etc. > is done interactively to make a better picture. > I hope this helps, > Elaine > > > On Sep 27, 2006, at 7:29 PM, Vishal Pua wrote: > >> Hi, I was wondering if there was a way to create a script, that >> would open pdb files, render them to look a certain way ex. wire >> or ribbon, then save, automatically? this would have to work for a >> number of pdb files? I have little programming experience, and >> wonder if there was an easy way to do this, thanks >> >> Vishal Pua >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev _______________________________________________ Chimera-dev mailing list Chimera-dev(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

1 0

Merge PDB Question
by Jared Godar 28 Sep '06

28 Sep '06

I have an incomplete pdb crystal structure of a homohexameric protein containing six ~25AA tails. In the incomplete model, two of these six tails are complete (A and F) and the other four are truncated at various positions (B,C,D, and E). I have used the either the A or F complete tails as templates and generated appropriate length segments to compleate each of the truncated B-E tails by selecting the appropriate residues and saving the selected atoms as a new PDB. Currently, I have all six tails completed and saved as a single PDB. I would like to use the Bond command to covalently link the extended chains, but my single PDB is segregated into models 1.1, 1.2, 1.3, 1.4, and 1.5. When I use the Bond command as follows "bond #1: 504.b@c & #1.3:505.a@n", I get an error that only one atom is selected. Does Chimera consider #1 and #1.1 to be different models? If so, how can I merge these 5 models into one to allow me to create the bond? Thanks, Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Department of Molecular Physiology & Biophysics 708 Light Hall 2215 Garland Ave. Nashville, TN 37232-0615 Work: 615.322.7898 Fax: 615.322.7236 jared.godar(a)vanderbilt.edu

2 1

Re: [Chimera-users] [chimera-dev] chimera help
by Elaine Meng 28 Sep '06

28 Sep '06

Hi Vishal, Actually you can do this with a Chimera command script, as opposed to programming in Python. A command script just contains the same commands you would enter in the Command Line. I'm not sure of what type of saving you had in mind, " but the "copy" command can be used to save an image file, "save" to save a session, and "write" to save a PDB file. This page links to all the command man pages, plus it discusses command scripts (at the bottom): http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/framecommand.html Just opening the command file will execute the commands. Here are links to a couple of example command files: http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/tutorials/ setup.com http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/ 1gfl.com And here is another, between the dashed lines: ----------------------------------------------------------------- open 1hxx open 1pho modelcolor coral #0 modelcolor cornflower blue #1 ~disp; rep bs; ribbon; ribrepr smooth matchmaker #0 #1 ----------------------------------------------------------------- I guess the main difficulty if you are saving images is how to get a good view of the structures. Usually some rotation, scaling, etc. is done interactively to make a better picture. I hope this helps, Elaine On Sep 27, 2006, at 7:29 PM, Vishal Pua wrote: > Hi, I was wondering if there was a way to create a script, that > would open pdb files, render them to look a certain way ex. wire or > ribbon, then save, automatically? this would have to work for a > number of pdb files? I have little programming experience, and > wonder if there was an easy way to do this, thanks > > Vishal Pua > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

how to get nonbonded distance and torsion angle list
by Prem Prakash Pathak 28 Sep '06

28 Sep '06

Hi! I am using the chimera for the visualizing protien form *.pdb file. I wanted to get the nonbonded distance , *.upl file and angle constraint files. Would you please help me in solving the problem. PremPrakash

2 1

"longbond" in scripts
by Eric Pettersen 26 Sep '06

26 Sep '06

We've made some improvements to the "longbond" command (breaks non- physical bonds that show missing structure segments) which are not backward compatible with the previous version. We are wondering if anyone makes any significant use of the longbond command in scripts. If you do, we would consider making a new command with the improved behavior and leaving the longbond command unchanged for backwards compatibility. So speak up if this affects you. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

Connolly surface and Triangulation
by Nihshanka Debroy 25 Sep '06

25 Sep '06

Hi, Not sure if this went the first time, so sending it again: ----------------------------------------------------------------------------------------------- I have been using Chimera to generate the Connolly surface for several different proteins and saving the surface information in X3D format. I was wondering what algorithms are used in the Connolly surface generation. Is it the same approach that Michael Connolly had come up with in his 1983 paper on Analytical Molecular Surface Calculation, or is it a variation of that algorithm? Also, when the surface information is saved by Chimera in X3D, it breaks the surface into triangular faces. I noticed that the coordinates of the points comprising the triangles are completely different from the atomic coordinates. I am interested in learning more about how the triangulation is created. If you could direct me to a link or paper that would help me better understand the algorithms involved in these two processes, that would be great! Thanks. Sincerely, Nihshanka

2 2

chimera ubuntu/debian package?
by Javier Díez 25 Sep '06

25 Sep '06

Hy: Is there a chimera version for ubuntu or debian? I would like to add the url to my sources.list if it exits. Thank you any way. Javi

2 1

Re: [Chimera-users] Map Oddities
by Thomas Goddard 22 Sep '06

22 Sep '06

Hi Albion, When you are running Chimera and it opens a Python code file with suffix .py and there is an older byte compiled version of the same file with suffix .pyc then Python automatically recompiles the .py file and you should see that the date on the .pyc file is updated. You never need to compile Python files by hand. Here are 3 ideas about how to make some programs that read MRC maps establish equivalent map positions. As I mentioned in my previous email some programs may fail with certain maps to associate the x,y,z axes with the correct data axes. And some may ignore all header info about positioning. So there are alot of different cases. I'm only going to make suggestions for the simple problems. One idea is to have Chimera print out the difference between the origin that a crystallography program would use versus the MRC 2000 origin. You could insert a little code in the Chimera mrc_format.py file to print this difference for MRC 2000 files. Specifically after the line self.data_origin = (v['xorigin'], v['yorigin'], v['zorigin']) add lines # Print difference between crystal and mrc 2000 origins ncs_nrs_nss = v['ncstart'], v['nrstart'], v['nsstart'] nxs, nys, nzs = ncs_nrs_nss[xa], ncs_nrs_nss[ya], ncs_nrs_nss[za] from VolumeData.griddata import scale_and_skew x0,y0,z0 = scale_and_skew((nxs,nys,nzs), self.data_step, self.cell_angles) print 'Origin difference ', self.name, '=', print x0 - v['xorigin'], y0 - v['yorigin'], z0 - v['zorigin'] The origin difference will be printed to the Chimera reply log and you can somehow apply it in other programs. A second idea is to try to modify the MRC 2000 map header so that the crystal origin is the same as the xorigin, yorigin, zorigin header values. This is generally not possible since the former uses integers while the latter uses float values. But if you don't care where the origin is as long as all programs agree, you might adjust xorigin, yorigin and zorigin to match the crystal origin. You would need some simple program to modify the map header. A third approach is to modify Chimera mrc_format.py so it never uses the MRC 2000 xorigin, yorigin, zorigin. If Chimera always uses the crystal origin that would probably more often agree with other software packages. I would recommend against this approach. You will later install a new version of Chimera without the modification and your fit PDB models will no longer align with their maps and you will probably forget why and scream. Tom > From: Albion Baucom <baucom(a)msg.ucsf.edu> > Subject: Re: [Chimera-users] Map Oddities > Date: Fri, 22 Sep 2006 17:12:51 -0700 > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Hi Tom, > Im going to take this off list since my inquiries get more specific > now, but you are welcome to post this back to list if you think it is > within the scope of the Chimera Users list. > > So, you were right. There is indeed a X, Y and Z origin field in the > map header. Thanks for pointing that out and giving me the code to > print those values to the reply log. > > A quick question regarding my modification to the mrc_format.py. I > don't know Python very well yet, and am wondering what happens when I > modified the source code. The modifications worked of course, but > Chimera did not recompile the code into a .pyc file. When are > the .pyc files accessed? > > OK, back to the original question :) > > So, offhand, could you suggest a fix for me so that other programs > that use the "other" origin can interpret the data the same as > Chimera? Naturally what is going to have to happen is I will have to > translate the PDB file a set distance based on the discrepancy > between the origin conventions. I would like to do this translation > as accurately as possible. > > What I noticed from an empirical re-docking of the PDB file into the > density in another program was it had to be moved approximately ~116A > in all 3 axes. This appears to be close to the following calculation > (for the x axis in this case) > > ( | xorg | - xlen) + (xlen/2) > > where xorg (-224) is the MRC2000 origin, and xlen (213.423) is the > xtal origin. In this case this comes out to be > > (224.000 - 213.423) + (xlen/2) = 117.289 > > Applying this to the model as a translation in all 3 axes looks > almost exactly like what I see in Chimera. > > Does this make any sense? This is all I could come up with that gave > an answer close to my empirical docking translation numbers. > > Thanks Tom. I really appreciate your help. > > Albion

1 0

Map Oddities
by Albion Baucom 22 Sep '06

22 Sep '06

Hi, I am trying to work out how maps are handled in various graphics programs so I can easily move between programs and expect to see the same thing in each session. Unfortunately at the moment that isn't working so well, and I would like to resolve this issue. Basically I have a situation where I have a PDB model and a CCP4 format EM density map in Chimera that are docked. When I open the exact same map and model in other programs such as O or Pymol, the map and the model are no longer in agreement. What I have noticed is that if I draw the unit cell for the map (P1 symmetry since this is an EM reconstruction), in Chimera, the model and map live in the center of the unit cell and are docked. If I draw the unit cell for O or Pymol, the map lives at the origin of the unit cell, at (0,0,0), which is in the corner, and model is outside of the unit cell offset by what appears to be some arbitrary translation (I have tried using half the unit cell dimensions as a translation, but that unfortunately gets me _very_ close to being correctly docked in the map, but off by some 10A). It appears Chimera is handling the map and model differently than the other packages and I am trying to get an idea of what happens when this map is loaded. I am including a listing of the map header from MAPMAN below. Thanks! Albion Grid = 96 96 96 Origin = -48 -48 -48 Extent = 96 96 96 Cell = 213.423 213.423 213.423 90.000 90.000 90.000 UVW = 1 2 3 Spcgrp = 1 Nr of points = 884736 Density min = -6.915E-01 Max = 2.397E+00 Average = 7.247E-11 Sigma = 2.290E-01 Variance = 5.243E-02 Mappage Prod= 8.257E+01 Plus = 57 Dyn. range = -6.903E-01 To = 2.398E+00 Cell vol. = 9.721E+06 Voxel vol. = 1.099E+01 Grid vol. = 9.721E+06 %Cell vol. = 100.00 Origin frac = -0.50000 -0.50000 -0.50000 Origin Cart = -106.712 -106.712 -106.712 Top frac = 0.48958 0.48958 0.48958 Top Cart = 104.488 104.488 104.488 Spacing = 2.223 2.223 2.223 Top = 47 47 47 Changes = F

2 3

Movement Mouse Mode Extension
by Jared Godar 22 Sep '06

22 Sep '06

I have installed the Movement Mouse Mode Extension, but I get the following error whenever I try to select anything other than the 'Normal' movement mode on the drop-down menu. ImportError: cannot import name functionCallables (see reply log for Python traceback info) Any insight on how I can get this feature to work for me? Thanks, Jared (Log info below) Traceback (most recent call last): File "C:\Program Files\Chimera\share\__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in init tkgui.eventLoop() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757, in eventLoop app.mainloop() File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 170, in <lambda> set_variable_cb = lambda v=self.variable, n=name: v.set(n) File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 780, in set self.tk_variable.set(value) File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 191, in set return self._tk.globalsetvar(self._name, value) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1751, in __call__ _reporterror(self.func, args) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1814, in _reporterror displayerror(msg) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1377, in displayerror _errorReportFile.write(text + '\n') File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 832, in cb callback() File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 800, in tk_variable_changed_cb cb() File "C:\Program Files\Chimera\share\MoveSelection\gui.py", line 64, in mode_changed_cb move.set_mouse_mode(mmap[self.mode.get()]) File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 569, in set_mouse_mode m = mover(create = True) File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 598, in mover the_mover = Selection_Mover() File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 36, in __init__ self.original_move_callbacks = self.wrap_mouse_modes() File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 42, in wrap_mouse_modes from chimera.mousemodes import addFunction, functionCallables ImportError: cannot import name functionCallables -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236

2 1

Connolly surface and Triangulation
by Nihshanka Debroy 21 Sep '06

21 Sep '06

Hi, I have been using Chimera to generate the Connolly surface for several different proteins and saving the surface information in X3D format. I was wondering what algorithms are used in the Connolly surface generation. Is it the same approach that Michael Connolly had come up with in his 1983 paper on Analytical Molecular Surface Calculation, or is it a variation of his algorithm? Also, when the surface information is saved by Chimera, it breaks the surface into triangular faces. I noticed that the coordinates of the points comprising the triangles are completely different from the atomic coordinates. I am interested in learning more about how Chimera creates the triangulation. If you could direct me to a link or paper that would help me better understand the algorithms involved in these two processes, that would be great! Thanks, Nihshanka

1 0

AMBER netCDF trajectory
by Mingfeng Yang 20 Sep '06

20 Sep '06

Dear Chimera developers, The latest release of AMBER supports netCDF format trajectory. Is there any plan for Chimera to support AMBER's new format? Best, Mingfeng

2 2

Chimera secondary-school use
by Thomas Goddard 19 Sep '06

19 Sep '06

Follow up on "[Chimera-users] first time use of chimera". ------------------ From: "Rich Kaufman" <richkaufmanpv(a)hotmail.com> To: goddard(a)cgl.ucsf.edu Subject: Chimera, afterthought Date: Tue, 19 Sep 2006 11:38:26 -0500 Dear Tom, Just to mention a few more details, I am trying to use electron density maps we generated in the lab using a Spider processing of cryo-EM photos .I will be downloading PDB's from the RCSB to dock with these. After properly hand docking the PDB, I will then load the density map and the hand-aligned PDB into a Normal Mode Flexible Fitting package ( NMFF ) for fine-tuning of the fit, to give a higher resolution picture of the electron density map. I've been working on this project for about three months. I had never heard of any of these things prior to that. It's been an amazing learning curve for me....quite interesting. Sincerely, Rich Kaufman, ( background....mainly physics; teacher of high school chemistry and physics ) P.S. One goal of this project is to enable me to use these techniques at the secondary education level. I don't know if that's doable....suggestions welcomed. --------------------- Date: Tue, 19 Sep 2006 10:00:38 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: richkaufmanpv(a)hotmail.com Subject: Re: Chimera, afterthought Hi Rich, Oh! I sent my previous email before I read this one about what you are actually doing. You're doing some fancy stuff. If you hand-align a PDB model in the SPIDER map you can then do a local position optimization within Chimera using menu entry Tools / Volume Data / Fit Models in Maps This moves the model using a rigid rotation and translation to maximize the map values at selected atom positions. Here's a page describing how to use it: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmod… The bottom of the following tutorial also gives step by step instructions for placing a PDB model in a map: http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/07-VolumeData/tut… In fact, most of the tutorials on the following page do this kind of fitting: http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html The normal mode fitting you will do is fancier, allowing the model to deform to fit into the map. The following page explains alot of the Chimera features for working with density maps. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html The myosin animation on the following web page shows fitting a model into a map: http://www.cgl.ucsf.edu/chimera/animations/animations.html Finally, here are some databases that show some cryo-EM maps of viruses and other systems. http://viperdb.scripps.edu/tnumlist.php?N=all http://www.ebi.ac.uk/msd-srv/emsearch/AccEMServ?criterion=Retrieve+All&valu… I'm sure this is more than you wanted to know! Tom

1 0

visualizing a confocal image stack
by William Beaver 19 Sep '06

19 Sep '06

Hello. I have a stack of intensity images (8bit) taken from confocal microscopy of dapi expression in Drosophila that I'd like to visualize. I cannot figure out the format that the volume viewer requires to view the data; more specifically, none of the formats in 'registered file types' are familiar to me and I've been unable to find anything about them to sort out which format I should convert to. I have read the image sequences into matlab (3d matrix) and can write output to just about anything from there if I know the format. Does anyone have an idea for what the best/easiest/only format I should use? A pointer to a spec on the format if it's not something trivial (like matlab 'save stack.txt varname -ascii') would be appreciated. If it makes a difference, at some point soon I'd like to visualize more channels that just dapi (dll, for example) simultaneously. Thanks in advance. I really do appreciate it! -William ------------ William Beaver wbeaver(a)cs.ucsd.edu

2 1

Re: [Chimera-users] Movie Question: EM Densities about robbon structures
by Thomas Goddard 18 Sep '06

18 Sep '06

Hi Jared, If you use Chimera commands that specify how many frames to rotate, shift, scale, fade over, ... then it does not matter how fast or slow your machine is. Each frame is recorded only after it is drawn, and none will be skipped. Only when you move a model by hand with the mouse will it matter how fast the machine is. Here are some problems with smooth transitions I have observed. Fading out a PDB model in stick mode produced all kinds of weird flickering of the bonds. This I believe is a bug in Chimera transparency of bonds and I plan on submitting a bug report for that. Smoothly changing the contour level does not produce a very smooth change in surface appearance. Little spots pop up or disappear at discrete contour levels. This is because the contouring algorithm (marching cubes) changes the surface triangulation in discrete ways when the contour level passes through a grid point data value. I don't know of any remedy although using surface smoothing (volume dialog under surface and mesh options) may help. Let me know what problems you encounter. I am interested in improving the Chimera movie capabilities. Tom > Date: Mon, 18 Sep 2006 13:11:39 -0500 > From: "Jared Godar" <jared.godar(a)vanderbilt.edu> > Sender: jared.godar(a)gmail.com > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Movie Question: EM Densities about robbon structures > > I did, thank you much... I have successfully installed the additional > extensions and am attempting to incorporate them into a .CMD script for my > movie. So far that is going fairly smoothly, with the exception of frames > involving fading in/out of structures are taking significantly longer than > others resulting in a jumpy movie. I'm going to attempt to try it on a > fastest machine and see if that helps. > > The independent rotation is working, the fade in/out of specific models is > good, and I'm going to try the contour transition next. > > Thanks again, > > Jared

1 0

first time use of chimera
by Rich Kaufman 18 Sep '06

18 Sep '06

9/18 To whom it may concern: I would like an abbreviated guide to loading a pdb and an electron density map into chimera for comparison and hand docking. I have only worked with visualization software for a few months and still, frequently, can't do what I want with it. Chimera was suggested as the easiest or perhaps only software to do what I need to do. Currently, I only have only got VMD downloaded, but can install chimera if its worthwhile. Sincerely, Rich Kaufman, U.KS. biochem. dept, Kansas City, Ks.

2 1

Movie Question
by Jared Godar 15 Sep '06

15 Sep '06

Hello there, I have a few technical questions about a movie I am trying to make with chimera. I have PDB files for three predicted structural elements of a larger protein whose structure my lab is resolving through cryo EM. I've converted these PDB files to MRC's of the desired resolution we are trying to obtain with the reconstruction. In an effort to produce animation which highlights structural elements of these three subdomains, I have encountered a couple difficulties translation the movie I envision through Chimera. I would like to start with the three subunits spaced across the X axis and rotating about the central y axis of each subunit. Then, one at a time, have a single unit grow and translate to the center, then while the other two subunits fade away, then return to it's original position. I've been able to script this type of motion for each of the individual subunits, but I hit a problem when I try to incorporate all three. - Is there a way to have multiple proteins roll about their own respective y axis instead of orbiting about the central y axis of the scene? - Is there a way to selectively show / hide (fade over specified number of frames) PDB's or MRC's like you can show / hide / fade text? Thank you in advance for your help. -Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236

4 4

Movie Question: EM Densities about robbon structures
by Jared Godar 15 Sep '06

15 Sep '06

Hello there, I have a few technical questions about a movie I am trying to make with chimera. I have PDB files for three predicted structural elements of a larger protein whose structure my lab is resolving through cryo EM. I've converted these PDB files to MRC's of the desired resolution we are trying to obtain with the reconstruction. In an effort to produce animation which highlights structural elements of these three subdomains, I have encountered a couple difficulties translation the movie I envision through Chimera. I would like to start with the three subunits spaced across the X axis and rotating about the central y axis of each subunit. Then, one at a time, have a single unit grow and translate to the center, then while the other two subunits fade away, then return to it's original position. I've been able to script this type of motion for each of the individual subunits, but I hit a problem when I try to incorporate all three. - Is there a way to have multiple proteins roll about their own respective y axis instead of orbiting about the central y axis of the scene? - Is there a way to selectively show / hide (fade over specified number of frames) PDB's or MRC's like you can show / hide / fade text? Thank you in advance for your help. -Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236

1 0

Dual monitor display
by John Hatten Jr. 15 Sep '06

15 Sep '06

Hi all. I'm a bit of a chimera newbie. I've been using DOCK for a while, and chimera has turned into a natural choice for combing through the results. I've noticed that chimera quits when I try to run it in dual display with XP. I get an error message that there is a driver conflict. Is there a way to fix this? I would love to have my display window on one screen and the tool windows on the other. Thanks for the wonderful software, its a great tool. Sincerely, John Hatten jahatten(a)duke.edu

2 1

16,000 molecules slow
by Thomas Goddard 13 Sep '06

13 Sep '06

Email exchange with Brittany Morgan about slow ball and stick display when displaying 16000 molecules. ---- From: "Brittany Morgan" <brmorgan(a)clarku.edu> To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: RE: [Chimera-users] Memory allocation Date: Tue, 12 Sep 2006 20:52:39 -0400 I am working with molecules, and it has problems redrawing them in ball-and-stick representation, although I expect that at larger system sizes other functions will start slowing down as well. If I look at the memory usage while it is redrawing them, Chimera seems to be using only about 1/4 of the available memory, but creating a paging file nonetheless. It will work, it just takes about 15 minutes to redraw about 64,000 atoms, and I need to go to system sizes much larger. If I need more memory, that is possible, I just wasn't sure if that was the issue because it didn't appear that Chimera was using all of the available memory. I am using Chimera in a non-standard way (I'm not displaying proteins, but rather many small (unrealistic) molecule-type objects). Thank you for your help! Brittany ----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Tuesday, September 12, 2006 9:22 PM To: brmorgan(a)clarku.edu Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Memory allocation Hi Brittany, Thanks for the detailed information. I do not think memory is the problem. Display of 58,000 atoms (pdb 1uf2) in ball and stick took 10 seconds on my 4 year old laptop. That is the time to make the intial drawing. Then it update at about 2 frames per second when rotating the model on this rather old machine. Your problem is likely caused by one of two issues. First, if your "molecule-type objects" contain many (tens or hundreds) small rings within a residue then Chimera will bog down trying to compute the chemical atom types (aromaticity...). This is a problem we have recently analyzed when using Chimera with molecules that do not have reasonable chemical structure. We plan on fixing this problem by being able to tag molecules in Chimera as "non-chemical". But we do not have a version of Chimera available with that feature yet. So currently the only solution is to modify your non-molecule model using multiple residues to avoid having many rings in a single residue. The ring computation is not done in wire display style but is invoked when switching to ball and stick style because atom radii are needed and are based on the chemical types. The second possible problem is that you are not using hardware accelerated 3D graphics. On Linux systems you usually need to install a graphics driver to get hardware acceleration. Windows and Mac systems usually already have the appropriate driver. Rendering computations can be 100 times slower if it is done in software instead of by the graphics chip. Ball and stick display style is much more time consuming to render than wire frame. If you are able to rotate the 64,000 atom ball and stick model after it is first displayed (15 minutes) and it updates reasonably fast (> 1 frame per second) then you have hardware acceleration and this is not the problem. Tom ----- From: "Brittany Morgan" <brmorgan(a)clarku.edu> To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: RE: [Chimera-users] Memory allocation Date: Tue, 12 Sep 2006 21:34:09 -0400 Hi Tom, I can rotate it after it is first displayed with no difficulty, so I would think that the problem is likely the first. My toy model molecules consist of 4 "atoms" in a linear configuration, so these are very small molecules, and I wouldn't have any rings within a residue, if I understand this correctly. However, would the fact that I have so many molecules be an issue (if I have 64,000 atoms, I have 16,000 molecules)? I can tell you more explicitly what I am attempting to display (and how) if that would be of use. Since I guessed, more or less, on how to output the data to get it to display what I want, it is likely that I am doing this in a less than optimal way. Brittany -------- Date: Tue, 12 Sep 2006 18:51:58 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: brmorgan(a)clarku.edu Hi Brittany, Ok it's not rings. Very likely something is slow when dealing with your large number of molecules. The typical Chimera use involves only a handful of molecules, twenty or thirty is considered alot, and 16,000 may be a record! Another Chimera developer Eric Pettersen will know more about efficiency with large numbers of molecules. (I work primarily on volume data.) So I've sent this email to him and he may have advice. If it is possible I think you would be better off making your 4 atom chains be a single residue with all chains in a single molecule. Chimera is likely to handle that much better. An immediate problem is that if you are using the PDB file format its residue number field is only 4 digits (max 9999 residues). It is awkward but you could use multiple PDB chain identifiers (single letter a-z, A-Z, 0-9) to handle up to ~600,000 chains. Another approach is to put all the chains in a single residue. But a residue with 64,000 atoms may also cause poor Chimera performance. I'll also warn you that Chimera is not at good as other molecular graphics programs (PyMol, and VMD) at handling systems larger than 100,000 atoms. Chimera uses much more memory (about 3 Kbytes per atom). PyMol and VMD I am told are 5-10 times more memory efficient on a per-atom basis. Chimera may be better for doing custom types of analysis though. Tom Is it OK if I forward your last email to the chimera-users mailing list? That may help others with similar problems. ----- From: "Brittany Morgan" <brmorgan(a)clarku.edu> To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: RE: [Chimera-users] Memory allocation Date: Wed, 13 Sep 2006 13:57:36 -0400 Hi Tom, Feel free to forward anything that you think would be of use to others. Unfortunately, 16,000 is only a moderately large system for me. I'm looking to be able to get up to around 112,500 atoms and a little under 30,000 molecules. I only need the visualization aspects of Chimera, all analysis I do on my own. Do you think PyMol would be able to handle something like that? I can try making them all a single molecule, but I also suspect that having a chain with 112,500 atoms would cause problems. Thanks again, Brittany ---- Date: Wed, 13 Sep 2006 11:07:59 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: brmorgan(a)clarku.edu Hi Brittany, There are two difficulties you are likely to run into: PDB file format limits on number of atoms (100,000) and number of residues (10,000), and poor software performance for such large systems. If you are primarily concerned with visualization rather than analysis than PyMOL I believe will give better performance. But you may have a hard time with the file format issues. I think you will get better support solving the file format problems with Chimera since we have 5 developers while PyMOL has just one. Having 100,000 atoms in a single PDB chain is not a problem. I believe also that Chimera can handle a modification of PDB file format where the atom number starts in column 6 instead of column 7 allowing up to 1,000,000 atoms. Eric would know. Tom ---- From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: brmorgan(a)clarku.edu Date: Wed, 13 Sep 2006 12:26:30 -0700 Hi Brittany, I confess I find your problem somewhat mysterious. I wrote a Chimera Python script (attached) that can either generate a single molecule with 16000 4-atom residues or 16000 4-atom molecules (depending on whether the 'singleMol' variable is True or False). While Chimera is better with the single-molecule system (on my mac, taking about 5 seconds each to run the script and to change to ball- and-stick), it isn't that much worse using the 16000-molecule system (about 20 seconds each -- not nearly 15 minutes!). It also took about twice as much memory (~1GB vs ~480 MB; this was using the 1.2255 snapshot). You can try it out yourself by using File..Open to open the script and changing the "singleMol = False" line in the script beforehand to choose modes. You should check that Chimera is using your graphics card rather than software rendering. One way to do that is to use Help->Report A Bug.. and click the Next button in the resulting dialog. The ensuing panel will have a "Bug Description" field that reports your OpenGL vendor and renderer. What does it say? If it says something involving "Mesa" then you are using software rendering and should try to update the driver for you card by visiting your card manufacturer's web site. You can click "Cancel" in the bug dialog to dismiss it. As Tom mentioned, we allow a modified PDB format where the sixth column of an ATOM record can be a digit, effectively allowing 1 million atoms. There are several gotchas in your situation. Whereas most such large systems are composed of standard residues with known connectivity, you may well need to specify your connectivity -- and CONECT records are strictly limited to 5-digit atom serial numbers. If your molecules do have typical bonding distances, you can let Chimera figure out the connectivity, but you would need to put each molecule in its own residue to prevent the N-squared intra-residue connectivity search from getting out of hand (so you would likely need to use chain IDs once you're past 9999 residues), and you would need to insert TER cards between residues to prevent the implied connectivity between residues (may not actually be necessary in the 1.2255 snapshot). --Eric File manyMols.py follows import chimera singleMol = False if singleMol: m = chimera.Molecule() m.name = "test" mols = [m] for ri in range(16000): r = m.newResidue("UNK", " ", ri+1, " ") prev = None for ai in range(4): a = m.newAtom("C%d" % (ai+1), chimera.Element("C")) r.addAtom(a) if prev: m.newBond(a, prev) crd = chimera.Coord(ri, ai, 0.0) a.setCoord(crd) prev = a else: mols = [] for mi in range(16000): m = chimera.Molecule() m.name = "test%d" % mi mols.append(m) r = m.newResidue("UNK", " ", 1, " ") prev = None for ai in range(4): a = m.newAtom("C%d" % (ai+1), chimera.Element("C")) r.addAtom(a) if prev: m.newBond(a, prev) crd = chimera.Coord(mi, ai, 0.0) a.setCoord(crd) prev = a chimera.openModels.add(mols)

1 0

Memory allocation
by brmorgan＠clarku.edu 13 Sep '06

13 Sep '06

Does Chimera have a fixed amount of memory allocated to it, and if so, is it possible to increase this amount? I am working with very large system sizes and am trying to reduce the amount of time it takes to perform certain operations.

4 3

Re: [Chimera-users] Memory allocation
by Thomas Goddard 12 Sep '06

12 Sep '06

Hi Brittany, Thanks for the detailed information. I do not think memory is the problem. Display of 58,000 atoms (pdb 1uf2) in ball and stick took 10 seconds on my 4 year old laptop. That is the time to make the intial drawing. Then it update at about 2 frames per second when rotating the model on this rather old machine. Your problem is likely caused by one of two issues. First, if your "molecule-type objects" contain many (tens or hundreds) small rings within a residue then Chimera will bog down trying to compute the chemical atom types (aromaticity...). This is a problem we have recently analyzed when using Chimera with molecules that do not have reasonable chemical structure. We plan on fixing this problem by being able to tag molecules in Chimera as "non-chemical". But we do not have a version of Chimera available with that feature yet. So currently the only solution is to modify your non-molecule model using multiple residues to avoid having many rings in a single residue. The ring computation is not done in wire display style but is invoked when switching to ball and stick style because atom radii are needed and are based on the chemical types. The second possible problem is that you are not using hardware accelerated 3D graphics. On Linux systems you usually need to install a graphics driver to get hardware acceleration. Windows and Mac systems usually already have the appropriate driver. Rendering computations can be 100 times slower if it is done in software instead of by the graphics chip. Ball and stick display style is much more time consuming to render than wire frame. If you are able to rotate the 64,000 atom ball and stick model after it is first displayed (15 minutes) and it updates reasonably fast (> 1 frame per second) then you have hardware acceleration and this is not the problem. Tom > From: "Brittany Morgan" <brmorgan(a)clarku.edu> > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] Memory allocation > Date: Tue, 12 Sep 2006 20:52:39 -0400 > > I am working with molecules, and it has problems redrawing them in > ball-and-stick representation, although I expect that at larger system sizes > other functions will start slowing down as well. If I look at the memory > usage while it is redrawing them, Chimera seems to be using only about 1/4 > of the available memory, but creating a paging file nonetheless. It will > work, it just takes about 15 minutes to redraw about 64,000 atoms, and I > need to go to system sizes much larger. If I need more memory, that is > possible, I just wasn't sure if that was the issue because it didn't appear > that Chimera was using all of the available memory. I am using Chimera in a > non-standard way (I'm not displaying proteins, but rather many small > (unrealistic) molecule-type objects). > > Thank you for your help! > Brittany

1 0

Re: [Chimera-users] Can I use "Chimera" to measure length of a VRML file?
by Thomas Goddard 12 Sep '06

12 Sep '06

Hi Masako, Chimera does not read IMOD files but perhaps I can add a file reader for you. Have you already defined a path in IMOD along the structure you want to measure? Or have you just segmented out the structures. If you have segmentations but no explicitly defined 1 dimensional path then it is not clear how to define the length. Is the IMOD format you are using the following? http://bio3d.colorado.edu/imod/doc/binspec.html Could you send me an example file? Tom > Date: Mon, 11 Sep 2006 17:41:20 -0700 > From: Masako Terada <mterada(a)ncmir.ucsd.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Can I use "Chimera" to measure length of a VRML > file? > > Hi. Thank you for your e-mail. I have tried using volume path tracer > as you instructed. Even though it looks very promising, it is > time-consuming since we have 90 different objects to measure. So I > would like to try your another suggestion, importing trace file into > Chimera and measure lengths. Are you familiar with IMOD segmentation > file format? I tried to import this IMOD file into Chimera, but > unsuccessful, so I am guessing that I have to convert it to something > else... Any more suggestion? > > Masako >

1 0

Can I use "Chimera" to measure length of a VRML file?
by Masako Terada 11 Sep '06

11 Sep '06

Hi. I have a VRML file, which was created with different softwares. Is there anyway I can use Chimera to measure length of this tube-like structure? Thanks, in advance! ---------------------------------------------------- Masako Terada National Center for Microscopy and Imaging Research Center for Research in Biological Systems University of California, San Diego (858)534-7968 mterada(a)ncmir.ucsd.edu ----------------------------------------------------

3 3

display multiple bonds
by Dave Roe 05 Sep '06

05 Sep '06

Is there a way to display multiple bonds so bond types (single, double, triple) can be distinguished? -- Dave Roe roex0050(a)umn.edu

2 1

color a residue
by Xuehong Liu 05 Sep '06

05 Sep '06

Hi, I chose the target as "selected residues", then selected the residue I want to put certain color on, but only a bond color was changed when I did that. However, if I did not select a residue, then the color option will change the color for the whole helix selected. thank Xuehong Xuehong Liu, Ph.D Research Assistant Professor Department of Physiology/Pharmacology Oregon Health & Science University 3181 SW Sam Jackson Park Rd. L334 Portland, OR 97239 phone: (503) 494-3230 fax: (503) 494-4352

2 1

PDB Coordinates
by Albion Baucom 01 Sep '06

01 Sep '06

I have docked several models into density manually using Chimera. I saved the session, reopened it, and when I write out the docked PDB files, and read them back in, they are not oriented the same way as the model I wrote them from. Is there something I have to do to "fix" their new orientation so when they are written out they retain this orientation? I am using beta version 1 build 2199 01/24/2006 on a linux platform. Thanks Albion

3 2

how to save a copy of the reply log via command line
by Cathy Lawson 01 Sep '06

01 Sep '06

Hi, I'd like to issue a command-line command within a python script read into chimera to save a copy of the reply log. I tried googling the chimera site but didn't find the answer--what would be the command to do this? thanks, Cathy

2 1

question about annealing residues in pdb file
by Shah, Sanket S 31 Aug '06

31 Aug '06

Hello, I have been using chimera extensively for pdb rendering and manipulation. I needed some information that i couldn't find in the archives. I am aware that chimera displays the pdb file according to the co-ordinates mentioned in the pdb file. However in my situation I have changed co-ordinates of some of the secondary structure elements like helices to do a better fit. and I have saved the new coordinates in the same pdb file. So now when i render this pdb file it shows me the structure with the modified orientation, however chimera displays a continuous model. In the sense, the breaks that I had introduced by changing the angles of some of the helices and thus making the linkage discontinuous are somehow annealed by chimera. So my question is what sort of algorithm chimera employs to seal breaks in the pdb structure. The same pdb strucutre when viewed in swiss model deepview software contains gaps/breaks at the junctions where the coordinates of the helices have been modified from the original ones. however no such breaks are seen when displayed through chimera. First I thought chimera does energy minimization to find out the best way to arrange the loops between the helices so as to create the best continuous structure. However it seems that chimera doesn't do energy minimization, yet it's able to display a complete structure. Could you please inform me about how this is accomplished. Thanks Sanket

2 1

change chain id
by Yunierkis Perez Castillo 28 Aug '06

28 Aug '06

Hi all, I need to change the chain ID for a protein, that is, change the chain A to chain B. Can I do that with chimera? Thanks in advance Yunierkis

3 3

addH/removeH for charged a.a.
by Dave Roe 26 Aug '06

26 Aug '06

Is there functionality that will - add a hydrogen (if needed) to all Lysines and Arginines to give the protonated form - remove a hydrogen (if needed) from Aspartic and Glutamic acids to give the deprotonated form? -- Dave Roe roex0050(a)umn.edu

2 2

Volume color zones
by hsosa＠aecom.yu.edu 21 Aug '06

21 Aug '06

Is is possible to use different colors for different Volume zones ?. I have a volume (MRC format) and have defined two marker sets using the Volume-Path-Tracer. Then I select one of the path and colored the surface volume around using the Volume Color Zone utility. This work fine but then if I selected the other markers and do the same the volume close to the new markers get colored but anything else get uncolored, including the areas previously colored. Am I doing something wrong ?. Can I color several Volume zones independently ? Thanks Hernando --

3 2

RealD (Stereographics) E2SGI emitter on Quadro 3450?
by Sabuj Pattanayek 18 Aug '06

18 Aug '06

Hi all, Anyone know if it's possible to use a RealD (Stereographics) E2SGI emitter on Quadro hardware? Thanks, Sabuj Pattanayek

2 1

addH utility and PDB files
by Nihshanka Debroy 15 Aug '06

15 Aug '06

Hi, I have a couple of questions about the addH utility built into Chimera, and about PDB files in general. I used addH to protonate (add hydrogens) to PDB files. Does it use a force field of some kind in the process, like Amber or Charmm? It seems that depending on the force field used to protonate a PDB, the values for the partial charges and the van der waals radii are different. Specifically, I am using these charges and radii in the DelphiController. Another thing I've noticed is that when adding hydrogens, for the same amino acid, the hydrogens are sometimes different in name or number. For example if I have a Cysteine, in some cases, an HG (gamma hydrogen) is added for the gamma sulphur, balancing out charges completely. In other cases, the HG is not added, and so the amino acid ends up with a net negative charge. I was just wondering if this is supposed to happen. Here's another example. For Alanine, I was getting 1H, 2H and 3H attached to the nitrogen in some cases. In other cases, I just got "H" attached to the nitrogen. Does this mean those particular instances of ALA in the PDB had one only hydrogen attached to the nitrogen, instead of 3 ? Wouldn't the missing 2 hydrogens lead to a net negative charge on the ALA? Thanks for all the help and for this mailing list. It is a wonderful resource. Sincerely, Nihshanka Debroy

2 1

Surfactant
by Annalisa Mercuri 14 Aug '06

14 Aug '06

Hallo everybody, I'm working with surfactants and emulsions. I'd like to use Chimera to reconstruct a micelle with my components, but I have no clue how to do that. Further my emulsion is made by a mixture of two surfactants. I would like to have a emulsion droplet image like the virus one. What do you suggest? Thank you for your help and advices Annalisa Mercuri MSc PhD Student School of Chemical Sciences and Pharmacy University of East Anglia Norwich Norfolk NR4 7TJ UK

3 2

structure slice
by Raquel Hernandez 14 Aug '06

14 Aug '06

Hello chimera e-mail, I have received from a colleague data set from a virus reconstruction. I am a novice in the use of your program but have managed to make an image of my virus. I would like to add an image of a slice of the virus through the center perpendicular to the three fold axis. Can you please advise me on what I need to do to make a slice? I can get the tech people here to help if you tell me the tools, etc that I need to use. Thanks. Raquel Raquel Hernandez Research Associate Professor Department of Molecular and Structural Biochemistry 128 Polk Hall North Carolina State University Raleigh, NC 27695 office:919-515-5765 lab: 919-515-5786 Fax: 919-515-2047

3 2

Fwd: Chimera and Macs
by Elaine Meng 14 Aug '06

14 Aug '06

Hello Mac users! When the Chimera window gets obscured by other windows on a Mac, clicking the X11 icon will bring it to the front (assuming you are using the recommended Mac/X11 version of Chimera). Begin forwarded message: > From: Kevin Dalby <dalby(a)mail.utexas.edu> > Date: August 13, 2006 11:54:43 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Chimera and Macs > > Hi Elaine > > I think we spoke briefly at the enzymes GRC. > > I am not a sophisticated chimera user. I use it on my mac while > working with another 10 programs . Usually i cant see the chimera > screen when i need it. Normally, when I want to get back to a > program that is hidden i go to the doc and just click on the > program icon and it comes to the front. This does not happen for > chimera. I know other spoilt mac users would enjoy a remedy. > > > best wishes > > Kevin > > > Kevin Dalby > Associate Professor of Medicinal Chemistry > University of Texas at Austin > tel 512-4719267 > fax 512-2322606 > > > > ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

spaceball
by Mario Halic 09 Aug '06

09 Aug '06

hi!, can I use spaceball 5000 as input device in chimera? thanks, Mario

2 1

Re: [Chimera-users] Electrostatic Potentials
by Thomas Goddard 08 Aug '06

08 Aug '06

Hi Nihshanka, Oops! My previous descriptions of how to determine electrostatic potential values at specific surface points assumed you were using the Surface Color tool to display the potential (menu entry Tools / Structure&Binding Analysis / Electrostatic Surface Coloring, or menu entry Tools / Volume Data / Surface Color). But you are using DelphiController and it has its own code for displaying potential values for which my previously described techniques will not work. To print the potential values at every surface point when the potential display was done with Delphi Controller you could put a print statement in chimera/share/DelphiViewer/MSMSTexturer.py at line 155, after the following lines of code else: # Point is outside of phi map. phivalue = 0 add the line print v_rs, phivalue Make sure the "print" line is indented the same as the "else:". This is going to print many thousands of lines in the Reply Log so be prepared to wait a bit. You could also use my previously described methods for showing potential values by using the Electrostatic Surface Coloring tool. Show a surface for your PDB model using Actions / Suface / show. Then in the Electrostatic Surface Coloring dialog press the "Open map data..." button and select the *.phi file generated by DelPhi (the one computed when running Delphi Controller). Then press the Color button on the surface color dialog. My previous code modification or the marker probe method could them be used. Tom

1 0

Electrostatic Potentials
by Nihshanka Debroy 07 Aug '06

07 Aug '06

Hi everyone, I have a couple of questions about the electrostatic potentials generated in Chimera using the Delphi Controller. If I have a protein with 5 chains A,B,C,D,E, and I choose to show the surfaces of all chains except C (but keep the wireframe of chain C's atoms) and then run Delphi using the DelphiController, does that mean that the potential surface generated is in the absence of chain C (which is what I want)? I'm trying to generate the potential surface without taking into account chain C, but would like to see C's wire frame for analysis purposes. Also, is there a way to get the actual potential values at each surface coordinate? Thanks a lot for the help. Sincerely, Nihshanka

4 3

coloring carbon and deleting hydrogens
by Narender Singh Maan 04 Aug '06

04 Aug '06

Dear all, I am trying to show two residues of a protein structure with 50% surface transparency along with a stick model (rest of the protein is 0% surface transparent). Now in this i am having trouble in showing those stick residues in a different color (for e.g. the default for C atom is gray, which i want to show in green). Is there anyway in which i can do it?. also for those two residues i want to delete the hydrogens (only in stick, and not in surface representation)? any suggestions would be of great help. Thank you

2 1

Coloring binding modes according to an energy term with ViewDock
by Vincent Zoete 04 Aug '06

04 Aug '06

Hi, Does it exist a way to color the different ligand positions obtained during a docking run, and displayed by the Viewdock module of chimera, as a function of a given energy term present in the columns of the viewdock table? If not, I think this could be an useful option to add to chimera. Also, it could be interesting to have the possibility to display the color scale as a function of the energy term together with the structures. If it cannot be done in the chimera display, it could be in the generated figures. Otherwise, congratulation for the great job the UCSF computer graphics lab is making with Chimera! Thank you for your time. Sincerely, Vincent

2 1

Re: [Chimera-users] X3D to VRML conversion
by Thomas Goddard 01 Aug '06

01 Aug '06

> Date: Tue, 01 Aug 2006 12:27:52 -0700 > From: Ben Morris > > Hey Tom, > > Were you using the chimera VRML viewer when you tested the new x3d2vrml > output? I had the same exact problem in my testing of the code before > submitting it, and Conrad told me that the Chimera vrml viewer is less > than perfect when it comes to complex geometry (surfaces and ribbons). I > don't know if you were using Chimera, or even if it is the only problem, > but when I tested the code using a third party viewer, ribbons and > surfaces worked fine! > > ~Ben Hi Ben, Yeah, I tested Chimera VRML output by reading it back into Chimera. I agree that the fact that ribbons did not display properly could very well be a problem with the Chimera VRML renderer rather than the output. I just displayed a Chimera round ribbon (1a0m) using FreeWRL 1.15 on Linux and it displayed correctly. It gave about 30 warnings like the following which may or may not be important: WARNING -- node Normal may not be ok as a field of type normal (...called from VRML::Field::SFNode, 1363) It sounds like you are the one who have worked on the Chimera VRML output rather than Greg. Thanks for working on this. I think it will be useful to many people. Tom

1 0

X3D to VRML conversion
by Nihshanka Debroy 01 Aug '06

01 Aug '06

Hi Dr. Meng, Thank you for your informative reply. That was very helpful. I was wondering if I could ask another quick question. I don't think that in Chimera, using the VRML format one can save non-surface information, like the backbone structure of a peptide (but one can display it). So I saved the information in X3D. And now, I'm trying to convert back to VRML format to be able to display it. I got completely lost when looking for some software to do this conversion. I tried using something called X3D to VRML97, but got a "segmentation fault" when I tried to open up the created VRML file. Has anyone faced this sort of an issue ? Thanks a lot, Nihshanka

2 1

about installation of Chimera in SUSE Linux 10.0 plateform
by Ching-Yi Hsieh 31 Jul '06

31 Jul '06

Hi, I have trouble to install Chimera in in SUSE Linux 10.0 plateform. Can you e-mail me the detail instruction about how to install soon??? Best, Dr. ChingYi Hsieh UCDavis Cancer Center

2 1

Chimera and DelphiController
by Nihshanka Debroy 31 Jul '06

31 Jul '06

Hi, My name is Nihshanka Debroy, and I am a graduate student at Duke University. I recently joined this mailing list. I was wondering if I could ask a couple of questions about the software. The first one is more related to Delphi. I have been using the Delphi Controller tool in Chimera, and I have been getting warnings that certain radii records are missing from my .siz file, and some residues have a net positive charge. I used the default files provided when installing Delphi. I was wondering if anyone has faced this problem before. Is there an online database where I could get the missing radii and charge values for atoms and residues ? Secondly, I am trying to generate the Connolly surface for certain proteins. What I have been doing so far is running Delphi Controller and assigning a probe radius of 1.4 Angstroms in the Parameter section. I just wanted to make sure that this is different from the molecular surface (MS) that is generated when simply choosing Actions->Surface->Show. Thank you for your time. Sincerely, Nihshanka

2 1

Segmentation Fault
by Donglu Xie 24 Jul '06

24 Jul '06

Hi All, Anybody has met this issue. When running chimera, it only shows "Segmentaion Fault", or " Segmentaion Fault (core dump)". No interface is shown. If you need more information about the system, please let me know. Any help is appreciated. Donglu Xie

2 2

Surface color key
by Alexander Rusnak 19 Jul '06

19 Jul '06

Hey Folks, I'm using Chimera to create a surface colored representation of a virus based on radius. That was not the hard part, my question is how do you make a key to show the scale of coloring. I cannot find that in the documentation, faq nor the server list. If it's there and I missed it sorry but you point it out to me and if it's not an option any suggestions on how to create one. Thanks. Alex

2 1

write out adjusted EM map?
by jbrown 19 Jul '06

19 Jul '06

Hi, I've recently used Chimera to manually fit several PDB subunits into my EM map. I am trying to figure out a way to write out the EM map in CCP4 format with the adjusted rotation/translations that I performed during my fit. Is there anyway to do this in Chimera (or are there any other programs you would suggest)? Also, any plans to include a means for writing out EM maps from Chimera in future versions? Thanks a lot, Jesse --------------------------- Jesse Brown Research Technician TSRI, Dept. of Cell Biology 858.784.8598 jbrown(a)scripps.edu

3 2

chimera on linux ia64 (sgi prism)
by Sabuj Pattanayek 14 Jul '06

14 Jul '06

Hi, I was wondering if there is a port for chimera to run on Linux IA64 (sgi prism)? The x86 version runs in emulation mode on the system, thus the graphics defaults to Mesa indirect glx (really slow). Would a dev be willing to port it for this system if given access to the system? I'm also working on getting pymol compiled for it. vmd already has a native port with good performance. Thanks, Sabuj Pattanayek

3 6

matchmaker command
by Haas, Ryan Matthew 10 Jul '06

10 Jul '06

Dear Chimera Users, How does the matchmaker command perform its superposition? Is it a C-alpha superposition, or just backbone atoms, or all atoms? Is it appropriate to use these RMSD values obtained from "mmaker" in a manuscript? Help is greatly appreciated. Matthew Haas

2 2

Re: [Chimera-users] script for residues w\in zone
by Eric Pettersen 06 Jul '06

06 Jul '06

On Jul 6, 2006, at 1:54 PM, Sorani, Marco wrote: > Thanks. I'm running Chimera and Python\IDLE on Windows XP. > > a) Can I still use the "script.com" you suggested? You could, by getting a UNIX-shell-like environment such as Cygwin (www.cygwin.com) or possibly just from the DOS prompt. If you don't care if Chimera's interface shows as the script runs, you could just run Chimera and then use File...Open to run the script. > b) When I try "script.py", I can't find the module "chimera" or > "chimera.py". Where should I look? script.py will only work if Chimera is the interpreter, rather than a stand-alone Python interpreter. So you need to either run "chimera -- nogui script.py" using methods like in the previous answer, or open the script using Chimera's main File...Open dialog. --Eric

1 0

script for residues w\in zone
by Sorani, Marco 06 Jul '06

06 Jul '06

Hi, A question: For a given PDB structure (say, 1J4N) and a given point mutation (say, C104K), I want to find all residues within 5 angstroms. Manually, this is easy to do with 'Select' --> 'Zone...', but if I have 1000 mutations, is there a way to automate the process and send results to a file? ****************** soranim(a)pharmacy.ucsf.edu Marco Sorani Program in Biological & Medical Informatics University of California, San Francisco

1 0

calculating charges for Dock
by Joshua D Campbell 28 Jun '06

28 Jun '06

Hello, My name is Josh Campbell and I'm trying to prepare a ligand for docking that is made up of non-standard residues using Chimera. The Dock Prep tool of course does not assign charges to non-standard atoms. I looked at your UserGuide and it said that there were other places to calculate non-standard residues using the Antechamber module, but I could not find any of these tools anywhere in the Chimera program. If you could give me some clarification as to adding charges on non-standard residues, I would be very greatful. I am working with "beta version 1 build 2199 2006/01/24". Thanks. Sincerely, Josh Campbell Harvard Medical School Laboratory of Structural Cell Biology

2 1

select certain transformants of multiscale models.
by Jonathan Hilmer 27 Jun '06

27 Jun '06

Actually, it is possible to use the command line to select portions of a multiscale-models generated volume set: it's just not really efficient. Open your structure and apply the BIOMT with multiscale models. Then select all the surfaces of the multiscale structure. Hide the surface representation and then show a ribbon representation. You might have to wait awhile for this to finish on a large structure. This will generate a new model for each subunit that can be selected manually, via command line, or with the model panel. You can then use the multiscale models panel to make color adjustments, show surfaces etc using selections defined in the command line. However, I can say from experience that learning the Python code is worth the effort in the long run. Jonathan > Hi, > > I'm wondering if it is possible to select specific volumes generated > via the multiscale model tool via the command line? E.g., for a set > of 60 biomt matrices I'm interested in coloring the chains generated > with matrices 1-20 in one color, matrices 21-40 in another color, and > matrices 41-60 in yet another color. Any suggestions on how to > accomplish this would be appreciated. > > thanks! > > Cathy Lawson > > > > *****************************************************************' > Catherine Lawson > Laboratory for Structural Biology and Bioinformatics > Department of Chemistry and Chemical Biology > 610 Taylor Road > Piscataway, NJ 08854 USA > http://roma.rutgers.edu > http://rutchem.rutgers.edu/~lawson > ***************************************************************** > > > > ------------------------------ > > Message: 2 > Date: Mon, 26 Jun 2006 18:18:57 -0700 (PDT) > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] selecting multiscale model volumes > To: cathy.lawson(a)rutgers.edu > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <200606270118.k5R1IvGE1909532(a)guanine.cgl.ucsf.edu> > > Hi Cathy, > > Unfortunately no Chimera commands allow selecting or coloring > multiscale surfaces. The multiscale tool in general is not well > integrated with the other Chimera capabilities -- like the Actions > Color menu won't color chain surfaces that you select with the mouse. > We plan on fixing this in the future but it may take a while (6 months > or more). > > Everything is possible using Python code, although this can be quite > difficult to figure out. It is not documented and the best approach is > to ask for examples from us that you can then modify. Below is code > to color multiscale surfaces with specific matrix subunits and chain IDs. > If you open that file in Chimera (with File / Open..., or with the "open" > command) it will do the type of coloring you requested. When you modify > the code be careful not to change the indentation since this is important > in Python. > > We could easily do a little better and add a Chimera command so that > you would not have to edit a Python script to specify what residue > ranges and colors to use. > > I am going on vacation tomorrow until July 18 but can make that > command for you when I return. It just requires some additional > Python code that Chimera will load at startup. > > Tom > > ---- > Python file mmcolor.py follows: > > # ---------------------------------------------------------------------------- > # Color certain matrix subunits and chains of a multiscale model. > # > def color_multiscale(rgba, model_num, matrix_nums, chain_ids = None): > > import MultiScale > d = MultiScale.multiscale_model_dialog(True) > for cp in d.chain_pieces(): > g = cp.surface_group > if g.model().id == model_num: > mnum, chain_id = g.oslName.split('.') > if chain_ids == None or chain_id in chain_ids: > if int(mnum) in matrix_nums: > cp.set_color(rgba) > > # ---------------------------------------------------------------------------- > # > red = (1,0,0,1) # Red, green, blue, opacity > green = (0,1,0,1) > blue = (0,0,1,1) > cyan = (0,1,1,1) > > color_multiscale(blue, 1, range(1,21)) # Color matrix subunits 1-20 > color_multiscale(cyan, 1, range(21,41)) # Color matrix subunits 21-40 > color_multiscale(green, 1, range(41,61)) # Color matrix subunits 41-60 > > # Example coloring subunits 1-20, only chains 'A' and 'B'. > #color_multiscale(red, 1, range(1,21), ['A', 'B'])

1 0

new snapshot release
by Eric Pettersen 26 Jun '06

26 Jun '06

We just put out another snapshot release (1.2255), principally to improve Antechamber reliability (particularly on Windows), but it nonetheless has a few other significant improvements: If you have Modeller installed, the Model Loops extension (very much under development) can fill in missing sections of structure. The defaults for Movie Recorder have been changed to improve playback performance and the ability to produce .avi files has been added. Multalign Viewer can add plain-text sequences to an existing alignment. Volume Viewer can display meshes as squares instead of just triangles. The "reset" command can interpolate between saved positions (i.e. positions in "savepos" commands) to ease creation of scripts involving motion. A new "Alignments" tutorial covers MatchMaker and Match->Align capabilities. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

selecting multiscale model volumes
by Cathy Lawson 26 Jun '06

26 Jun '06

Hi, I'm wondering if it is possible to select specific volumes generated via the multiscale model tool via the command line? E.g., for a set of 60 biomt matrices I'm interested in coloring the chains generated with matrices 1-20 in one color, matrices 21-40 in another color, and matrices 41-60 in yet another color. Any suggestions on how to accomplish this would be appreciated. thanks! Cathy Lawson *****************************************************************' Catherine Lawson Laboratory for Structural Biology and Bioinformatics Department of Chemistry and Chemical Biology 610 Taylor Road Piscataway, NJ 08854 USA http://roma.rutgers.edu http://rutchem.rutgers.edu/~lawson *****************************************************************

2 1

Making aliases persist
by Jeramia J Ory 26 Jun '06

26 Jun '06

I have some students this summer who are using Chimera to check out ligand anomalies in the PDB, and have fallen in love with the 'alias' command, no surprise. Is there a way to have them persist between sessions, or save them in the preference file somewhere? I imagine piling them all into a file and then having them 'read' it each session would work, but I thought I would see if there is a better way. Thanks, Jeramia Ory

3 2

question
by Jaya Bhatnagar 26 Jun '06

26 Jun '06

Hi, Is it possible in chimera to define a new amino acid residue? Also, what algorithms does it support involving docking of two proteins? And is there a limit on number of amino acids present in the protein? thanks a lot, Jaya

3 2

Selecting from a surface area
by Miguel Ortiz-Lombardia 26 Jun '06

26 Jun '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I'd like to pick an area of a (msms) surface (like with a "lasso" tool) and from that area, select the atoms/residues from which it is built. I haven't found anything like this in the documentation, so I'm afraid it's not possible. Or is it? Best regards, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (Darwin) iD8DBQFElFsPF6oOrDvhbQIRAiLYAJ9NHoF7sHbXJnZijo9Gfv8z9HJatQCfb9XQ 9q3hYNVjsZjVslF3Hv9+8ZU= =5dnB -----END PGP SIGNATURE-----

2 1

Re: [Chimera-users] question
by Goel, Manisha 26 Jun '06

26 Jun '06

Hi Elaine, I too have been looking for a good protein-protein docking program, so I am jumping on the bandwagon .. Just small question regarding point 2 in the mail .. Does chimera do any minimization/optimization of the complex after we manually dock the two protein together ? Thanks a lot for your help.. Regards, -Manisha -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Elaine Meng Sent: Monday, June 26, 2006 11:34 AM To: Jaya Bhatnagar Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] question Dear Jaya, (1) Chimera will display whatever coordinates and residue names are present in the input file. It does not matter if the residues or the atoms in them are standard or not. However, you cannot define new residues to be built by Chimera with the "swapaa" or "addaa" commands. We have recently added a Build Structure tool (Structure Editing category) that lets you add arbitrary atoms and bonds to structures interactively. It is in the early stages of development, however, and is likely to change in the future. If you use this, you may want to check the bond lengths and adjust them in the "Set Bond Length" section of the Build Structure tool. The man page for Build Structure: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html (2) Chimera does not do any automated docking. However, you can manually/interactively dock structures by moving one relative to the other (to freeze a structure and move only the others, you would uncheck its Active button in the Model Panel or its checkbox under the Command Line). The man page for the Model Panel: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html (3) I believe there is no limit on the number of amino acids present in the protein. There may be limitations due to the input file format (that is, the residue number column can only be a certain width in the input file format, usually PDB). However, in combination with use of different chain IDs this limit is quite high. For example, ribosome structures can be viewed in Chimera, although it may take a while for the structure to load. I hope this helps, Elaine On Jun 23, 2006, at 8:06 AM, Jaya Bhatnagar wrote: > Hi, > Is it possible in chimera to define a new amino acid residue? Also, > what > algorithms does it support involving docking of two proteins? And > is there > a limit on number of amino acids present in the protein? > > thanks a lot, > Jaya > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 38, Issue 12
by Jonathan Hilmer 16 Jun '06

16 Jun '06

Thanks to all for the quick responses on interpolation. Here's a quick example showing what I was concerned about: arrows.bld ------------------ .color red .arrow 0 0 0 1 0 0 .color green .arrow 0 0 0 0 1 0 .color blue .arrow 0 0 0 0 0 1 ------------------ matrix2 ----------------- Model 0.0 0.505641 0.433743 -0.745785 -2.58211 -0.807506 0.542275 -0.232105 2.90884 0.303746 0.719587 0.624446 -0.194334 ----------------- matrix3 ---------------- Model 0.0 0.60158 -0.458982 0.653787 0.653219 0.190507 -0.712397 -0.675423 5.48737 0.775763 0.530872 -0.341124 0.0103466 ---------------- The first matrix is just unity. The 'reset'-based interpolation works great for going between 1 and 3 or 1 and 2 in both directions, as well as 3 to 2, but fails from 2 to 3. Since all this is new to me, I can't say for certain that this is due to gimbal lock, but that was my first guess. I haven't had the opportunity yet to try out Tom's axis-angle approach, but that should rule out any Euler problems. The other problem for me is that all my current methods are based upon a stepwise approach via commands (ungainly, but very functional when combined with shell scripts, imagemagick etc), and this is incompatible with the 'reset' interpolation. Perhaps it was misleading to mention the use of 'matrixset'. I appreciate that it is more trouble to deal with external files, but if it is not possible to easily implement the interpolation I'm looking for dynamically within Chimera's Python (due to required math libraries, etc) then I would have to hard-code the interpolation matrices into the .py script file anway, defeating the purpose. Thanks for the help: I'd love to hear about any future development in this area.

3 2

Chimera paper virus models
by Thomas Goddard 16 Jun '06

16 Jun '06

Hi Ulrich, This week I made 5 paper virus models using the Chimera flatten icosahedron tool. You can have the images I created: http://www.cgl.ucsf.edu/home/goddard/temp/viper-gallery-jun2006/ The image files are named according to the Protein Data Bank (PDB) 4 letter id code. The page http://www.cgl.ucsf.edu/home/goddard/temp/viper-gallery-jun2006/vipergaller… shows images of the approximately 200 known virus capsids taken from the VIPER web site. http://viperdb.scripps.edu/ I added some comments to the flatten icosahedron documentation a few days ago describing "tiling" of the Chimera image to handle capsid proteins that are cut in half -- so they appear on both sides of the cut. http://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.h… I printed my images on standard photopaper. The images above will need to be scaled to fit on a piece of paper. I just asked my web browser to scale them to fit when I printed. One additional note about my images -- I turned on "silhouette edges" to give the black outlines around the proteins. This is done using Chimera menu entry Tools / Viewing Controls / Effects. Tom

1 0

Chimera movies in PowerPoint
by Thomas Goddard 16 Jun '06

16 Jun '06

Hi Xinchao, Several people have asked exactly your question of how to get a Chimera movie to play in PowerPoint on Windows without being jerky. I don't have a Windows machine to test on today but I investigated on the web and have a theory. I believe the jerky playback is because Chimera is encoding the movie using the -qscale option to the ffmpeg encoder causing variable bit rate (VBR) encoding. When you play the movie it becomes jerky because the player software does not handle the variable bit rate well -- it doesn't buffer up enough data and then can't handle the passages when alot is changing in the video. Another issue is choosing a format that PowerPoint on Windows accepts. Here are two suggestions. The first is to reencode the movie using the ffmpeg program included in Chimera: chimera/bin/ffmpeg -i mymovie.qt -f avi -vcodec msmpeg4 -b 2000 mymovie.avi This command produces an AVI file using msmpeg4 encoding at a bit rate of 2000 Kbits / sec (about 12 Mbytes / minute) from a quicktime file created by Chimera. You can increase the bit rate to get better quality or lower it to get smaller file size and worse quality. From what I read on the web Windows XP will be happy with AVI format and msmpeg4 encoding. You may find it hard to run this command unless you are familiar with running command-line programs on Windows. You could use a Windows Command Prompt window or Run Command, but you may need to provide full paths to the ffmpeg program and movie file. An alternative is to modify the Chimera Movie Recorder code chimera/share/MovieRecorder/ffmpeg_encoder.py putting comment characters (#) in front of lines 106-111: arg_list.append('-qscale') qsc = param_dict['Q_SCALE'] if qsc: arg_list.append(str(qsc)) else: arg_list.append('1') so they become # arg_list.append('-qscale') # qsc = param_dict['Q_SCALE'] # if qsc: # arg_list.append(str(qsc)) # else: # arg_list.append('1') This change is eliminating the -qscale option when Chimera runs ffmpeg to encode your movie. Instead we will explicitly request the encoding bit rate with the -b ffmpeg option. Now restart Chimera and record a movie with the Movie Recorder using "Custom" video format to select bit rate (which controls movie quality and file size). The Custom video format settings are under the Movie Options panel, swich on "Use preset video format" and select "Custom" from the Presets menu. Then set the resolution to match your Chimera window size (shown in the upper right corner of the Movie Recorder dialog, choose the encoding format and set the bit rate (in kilobits per second). If you don't make these Custom settings then Movie Recorder will use ffmpeg's standard very low bit rate of 200 kbits/second making a very low quality and small file size movie. Let me know if you found either of these suggestions to produce usable movies for PowerPoint on Windows. Then I can change Chimera Movie Recorder to make it easy to use such settings. Tom > To: goddard(a)cgl.ucsf.edu > Subject: Chimera Movie format > Date: Fri, 16 Jun 2006 15:33:52 -0400 > From: Xinchao Yu <yxinchao(a)bu.edu> > > Dear Tom: > I am a graduate student working with Dr. Christopher Akey at Boston > University. Recently, I have been trying to make some movies for large > compplexes with multiple domains. My problem is that if I use MPEG as the > output movie format, the movement can get very jerky in the movie. While I > don't have this problem with .mov format (compressed to the same extent as > the .MPEG files). But .mov file is not readily incorporated into powerpoint > presentations. Did you have similar observations? Or do you have some > suggestions concenning this problem. Thanks a lot! > > > Xinchao Yu > Department of Physiology & Biophysics > Boston University, School of Medicine > 700 Albany Str., Boston, MA, 02118 >

1 0

matrixget/set, keyframes, and interpolation
by Jonathan Hilmer 16 Jun '06

16 Jun '06

Does anyone have experience making movies in Chimera used more advanced motions, besides the standard roll, rock, etc? My general idea is to use matrixget to output a series of matrices, interpolate them in my standard Python environment (which is related to the question from Vol 38, Issue 10), and create as output a Chimera script composed of hundreds of 'matrixset' matrices. The Python Computer Graphics Kit (http://cgkit.sourceforge.net) will give me the functions for quaternions, as would ScientificPython or pythonOpenGL, but a quick review of their documentation suggests that in any package it will be necessary to interpolate the rotation separately from the translation: obviously it would be more convenient if there is a package that can transparently interpolate the matrices as provided by Chimera. Has anyone gone through this issue before, hopefully with some tips for me? Thanks, Jonathan

4 3

how to tell chimera to use the local python installation
by Sabuj Pattanayek 15 Jun '06

15 Jun '06

Hi, With the release of xorg-7.1.1 and mesa-6.5 I finally have direct rendering for my i855gm/i810 intel video device under linux. However I get lots of flickering of an object inside of the chimera display window when I rotate or move the object. I don't have this issue with pymol (compiled against the system python) and vmd (compiled against C/C++ opengl bindings?) or even glxgears. Perhaps I can workaround this problem by telling Chimera to use the local python installation? How is this done? Thanks, Sabuj

2 1

saved image discoloration
by Megan Grabenauer 13 Jun '06

13 Jun '06

I've successfully used Chimera in the past to make beautiful images for publication. However I recently installed v1.2199 for Mac OS X and now whenever I try to save an image I get discolored boxes throughout the saved image. (see attached) The position of the boxes varies slightly each time. I have the image width set to 1050 pixels, 300 pixels per unit, and supersample at 3x3. Any suggestions would be appreciated. I do have an older computer, is this possibly a hardware issue? Megan

2 1

Dock PDB into low resolution EM map.
by Puey Ounjai 12 Jun '06

12 Jun '06

Dear all, I am trying to dock atomic coordinate of a protein derived from 3D X-ray crystal (PDB format) into lower resolution (about 20-25 A resolution) EM map (BRIX, XPLOR ASCII or SITUS format) from 2D crystal. 1. Does Chimera have this kind of fitting tool (PDB to volume) or I have to fit the coordinate by hand? If chimera can do this task, Which command should I use? 2. Does Chimera have any statistical evaluation for manual fitting? 3. How can you evaluate the % matching of 2 models in Chimera? Best regards, Puey Ounjai

3 2

Fish-eye view
by Thomas Goddard 12 Jun '06

12 Jun '06

Hi Gabe, Fish-eye would be handy for presentation images. I submitted a request for this in 2003 to the Chimera bug/feature tracking system. Unfortunately it has not seen the light of day since. But I make fish-eye images once in while. I've attached one I just made for you as a test looking inside reovirus (1ej6). The trick is to bring up the Chimera Python shell, menu entry Tools / General Controls / IDLE and type a few things: >>> c = chimera.viewer.camera >>> c.viewDistance 30.0 >>> c.screenWidth 13.0 >>> c.viewDistance = 2 >>> The parameters that control the field of view are "viewDistance" (default 30) and "screenWidth" (default 13). I think view distance means how far your face is from your screen and screen width is how wide the Chimera window is -- maybe the defaults refer to centimeters. The defaults (narrow screen and far view) give a field of view of 25 degrees. Setting viewDistance = 2 gives a field of 150 degrees. Tom > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > From: Gabriel Lander <glander(a)scripps.edu> > Subject: odd request > Date: Fri, 9 Jun 2006 13:03:11 -0700 > > Hi Thom, > The P22 paper I presented at the biophysics conference in Salt Lake > City will be published on June 23rd in Science, so when that happens > I'll send the movie I made with Chimera your way. > We actually got the cover of the issue, and I worked with a graphics > artist here at scripps to put it together using his fancy graphics > software. One thing that really made the structure very visually > striking was the implementation of a fisheye lens. Although this > feature is not scientifically very useful, it would be a great artistic > addition to Chimera. I have no idea how difficult this would ever be > to implement or if it'd be worth it, but it's just a thought. I know > you get like a million suggestions a day, so obviously this would go > somewhere in the utmost bottom list of things to do. > I've attached the mockup we made for the cover to give you an idea of > what I'm talking about. > Cheers, > -gabe > > *** removed image ***

2 1

Colored Rays
by Mark Cunningham 12 Jun '06

12 Jun '06

Elaine, thanks for your response to my question on the coordinate system problem. My problem, as you suggested, was not related to coordinate systems, rather there was a problem with GOLD writing extra coodinates (electron pair coordinates) to its output file, which caused the structures to have enormously large rmsd, so much until the GOLD ligand appeared to be in a different coordinate system relative to the reference ligand. After going in and deleting the extra coordinates, everything worked fine. But now I have another question. Occassionally, while visualizing and manipulating a protein structure (1XAP) with Chimera, I get colored rays (30-40) stretching across the screen. Is this a bug in the program? How can I stop this from happening? If I close Chimera, and open it again, it works for a while, and then sporadically the rays reappear. Thanks. Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

2 1

Sporadic Colored Rays Across Screen
by Mark Cunningham 11 Jun '06

11 Jun '06

Elaine and Eric, thanks for your responses to my question on the coordinate system problem. My problem, as you suggested, was not related to coordinate systems, rather there was a problem with GOLD writing extra coodinates (electron pair coordinates) to its output file, which caused the structures to have enormously large rmsd, so much until the GOLD ligand appeared to be in a different coordinate system relative to the reference ligand. After going in and deleting the extra coordinates, everything worked fine. But now I have another question. Occassionally, while visualizing and manipulating a protein structure (1XAP) with Chimera, I get colored rays (30-40) stretching across the screen. Is this a bug in the program? How can I stop this from happening? If I close Chimera, and open it again, it works for a while, and then sporadically the rays reappear. Thanks. Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

1 0

Reading Frame Problem
by markcunningham 10 Jun '06

10 Jun '06

Could someone please help with this. . Using Chimera, I am trying to calculate rmsd between an observed ligand versus GOLD docked ligand, however the problem is the ligands load into different reading frames. The format for both ligands is .mol2. How can I correct this problem, in other words load both ligands into the same reading frame so that I can then calculate their rmsd. Thanks. Mark

3 2

Reading Frames
by Mark Cunningham 09 Jun '06

09 Jun '06

Hopefully someone can please respond to this before the weekend. I have Windows version of Chimera. I am using Chimera to run rmsd between observed ligands and GOLD calculated ligands. When I open both ligands ( with .mol2 format) with Chimera, they load in different reading frames, thus I can't make the rmds calculation. Please address this issue. The rmsd works fine otherwise, its just with the GOLD ligand files that I am getting the reading frame problems. Thanks very much. Mark Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

1 0

Writing a .x3d file that other programs can read
by Esther Bullitt 07 Jun '06

07 Jun '06

Hi, I am having trouble exporting a .x3d file in a format which programs that convert .x3d data to VRML data can read. The error message for one of them is: Xj3D Version: 1_0 Device found: Mouse-0 Device found: Keyboard-0 Error: Unexpected Exception: Unknown field name: chimera:hither for node: org.web3d.vrml.renderer.ogl.nodes.navigation.OGLViewpoint@1080876 Error: Failed to load file -- The ultimate goal is to have a VRML file that includes both the EM surface map and the pdb subunit structure together in a file that can be read by one of the companies that laser etches the structure into a glass cube. Some companies can read the pdb, some the VRML, but none can read both. Chimera says the .x3d can be converted into .vrml if there are no clipping planes or perspective, which there are not. But I still get this error. Any suggestions, pls? thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics, Room W302 Boston University School of Medicine 715 Albany Street (mail only; couriers use 700 Albany Street) Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041

2 1