- Chimera-users - RBVI Mailing Lists

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

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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.

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