- 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

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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

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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

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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)

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

29 Jan '07

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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

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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?

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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

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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 >

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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

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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

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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)

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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 ?

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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.

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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