July 2012 - Chimera-users - RBVI Mailing Lists

Scripting headless Chimera
by Evans, Mark 06 Jul '12

06 Jul '12

Hello, I am doing some epitope analysis and I am generating images of each potential epitope overlaid and colored on the antigen model. I have a script that loops through a list of residue sets (epitopes) and uses chimera to generate the images. The script works if I call it from within Chimera running on Mac OSX. I just installed the headless version on Redhat linux and was trying to modify my python script to run on the headless version and I ran into a few issues I would like some advice with. 1. Say I have ten sets of residues, which should produce 10 images. I get the first one, but then I get the following error: Traceback (most recent call last): File "/opt/bin/Chimera64-1.6.2rc/share/chimeraInit.py", line 686, in init midas_text.doRunScript("runscript", script) File "/opt/bin/Chimera64-1.6.2rc/share/Midas/midas_text.py", line 2037, in doRunScript execfile(scriptPath, scriptGlobals) File "batchEpitopeModel3.py", line 144, in <module> callChimera(data[ab][4],data[ab][5],fn,dn) File "batchEpitopeModel3.py", line 29, in callChimera rc("open " + trimer) File "/opt/bin/Chimera64-1.6.2rc/share/chimera/__init__.py", line 2426, in runCommand makeCommand(*args, **kw) File "/opt/bin/Chimera64-1.6.2rc/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/opt/bin/Chimera64-1.6.2rc/share/Midas/midas_text.py", line 1427, in doOpen modelArg, noprefs) File "<string>", line 1, in <module> File "/opt/bin/Chimera64-1.6.2rc/share/Midas/__init__.py", line 1937, in open raise MidasError('%s' % msg) MidasError: No such file or directory Error while processing 'batchEpitopeModel3.py': MidasError: No such file or directory File "/opt/bin/Chimera64-1.6.2rc/share/Midas/__init__.py", line 1937, in open raise MidasError('%s' % msg) It seems like Chimera terminated my script, even though it should be executing a loop. 2. The images that are generated on the Mac are large, hi-res pngs, but the images generated by the headless version are very small, low-res versions. I am not setting any image dimensions, are the defaults different between the two versions? Thanks for any help. I can post (or email directly) part of my python code if that is helpful. -Mark -This e-mail and any attachments may contain CONFIDENTIAL information, including PROTECTED HEALTH INFORMATION. If you are not the intended recipient, any use or disclosure of this information is STRICTLY PROHIBITED; you are requested to delete this e-mail and any attachments, notify the sender immediately, and notify the LabCorp Privacy Officer at privacyofficer(a)labcorp.com or call (877) 23-HIPAA / (877) 234-4722.

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Surface rendering
by George Tzotzos 06 Jul '12

06 Jul '12

Hi everybody, I'm using SiteComp to detect differences in binding affinities between two similar structures. The _clusters.pdb file produced by SiteComp is a standard PDB file in which the grid points corresponding to the difference clusters are represented by hydrogen atoms. They can be treated as any molecule in Chimera. Usually I find it useful to represent them as a mesh surface. Usually, I load in Chimera the protein.pdb, the ligand.pdb and the _clusters.pdb. After this, I select the _clusters.pdb and show it as mesh or solid using Actions-> Surface. In some cases, I fail to render the surface, or to be precise only one part of the clusters is rendered. I understand that this is a frequent problem with this type of discontinuous pdb. I'm attaching one such file and I would be grateful for any help Best regards George

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Generating binaries in Chimera Python
by Raju Purohit 06 Jul '12

06 Jul '12

Hello, I am working on SWIG which converts the functions written in C and C++ into their python equivalent which would be later used in Chimera. At one point while building binaries, I received an error message saying *extensions must be built with a compiler than can generate compatible binaries. Visual Studio 2003 was not found on this system.* So I believe installing Visual Studio 2003 must help building binaries. But since I will be actually working on Chimera Python, I wanted to know which compiler can generate compatible binaries in Chimera Python? Shall I go ahead with Visual Studio 2003? or any other version? Thank you in advance. -- Raju R.N. Third Year, B.Tech Mechanical Engineering National Institute of Technology Karnataka, Surathkal

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how to use the command of "savepos" and "scene"
by Qinfen Zhang 05 Jul '12

05 Jul '12

Dear All I'd like to use the commond "savepos" or "scene" to save the maps' rotations and translations relative to input coordinates, etc., but when I used the command: ~savepos ****(a name I write) , or ~scene ***** There are errors reminder:No position named *****, or No scene named **** The versions I have tried include 1.6.1-linux_x86_64 and 1.6.2-linux_x86_64. Both of them have same problems. Could you kindly tell me how to use the savepos or scene, or how to resolve my problems? Millions thanks Qinfen ************************************************ （Qinfen Zhang）（Ph.D） Bio.EM.Lab,School of Life Science, Zhongshan（Sun Yat－sen） University Guangzhou, 510275,P.R.China Tel:86-020-84112286(Lab) http://scholar.google.com/citations?user=Wj62cPoAAAAJ&hl=en http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=80 http://bioem.sysu.edu.cn ************************************************

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Re: [Chimera-users] question about surface properties in Chimera
by Elaine Meng 05 Jul '12

05 Jul '12

Hi Katie, The hydrophobicity coloring in the presets menu is simply using the Kyte-Doolittle amino acid hydrophobicity values. That is, all the surface patches belonging to a given amino acid residue type will have the same color, and the colors range from blue for the most hydrophilic through white to orange-red for the most hydrophobic. If you open Render By Attribute (under Tools... Structure Analysis) and set it to show the attribute of "residues" named "kdHydrophobicity" you can apply a different coloring scheme to these same values. Or, if you want, you can write out a file that lists the residues in the protein and the associated values (in that tool's menu, use File... Save Attributes). That will include all the residues, though, not just the ones on the surface. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html…> However, as mentioned, it is merely a lookup based on the residue type. There is a table of Kyte-Doolittle hydrophobicity values here, and instructions for using different scales of amino acid hydrophobicity, if you would like: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> We encourage Chimera questions to be sent to chimera-users(a)cgl.ucsf.edu (Cc'd) unless the message includes private data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 4, 2012, at 7:40 AM, Katherine Klymko wrote: > Dear Dr. Meng, > Hello--I am a theoretical chemistry student at Columbia University and I am interested in the hydrophobicity maps of proteins that Chimera generates: I know that this can be used to visualize the hydrophobicity of the surface, but does it also generate a file that I can use that lists the positions of the surface atoms or amino acids with their hydrophobic value? I am interested in quantitatively comparing the hydrophobic surface organization in a large number of proteins. > > I apologize if you are the wrong person to ask but when searching for solutions on line, you seemed to be the person that a lot of people went to for help. > Thank you, > Katie Klymko

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just a word of appreciation
by Reut S. Abramovich 05 Jul '12

05 Jul '12

Hi, Just wanted to say i have been using chimera for the last 6 years or so, and enjoy it very much. I hope you will continue to improve this magnificent scientific tool - its doing a great job in balancing a logical, easy to use, user interface and providing the user with a lot of impressive capabilities, which i can run on my laptop (and thats important !!). I really think Chimera team should be congratulated not only on content and code writing, but also on project management. All the best ! -- Kind Regards, Reut S. Abramovich PhD candidate Australian Centre for Astrobiology University of New South Wales Room G13, Biological Sciences Building Kensington, NSW 2052, Australia Phone: (+61) 02 9385 2098 Cell: (+61) 0406 858 646

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Error when exporting to obj format
by Vicente Díaz 05 Jul '12

05 Jul '12

Hi: I am trying to export a scene to obj format. I have tried this export with two different versions of chimera (1.5.3 and 1.6.1), and tried to open the resulting file in two different 3d programs: Cinema 4D and 3d studio max. Although both applications recognize the exported file, when they open it they dont find any content. In C4D, the file is an empty scene, while importer in 3ds max sends an error message telling that there are no objects to import. Therefore, it seems that the file is empty. I have seen that this kind exporting in Chimera is too fast (almost instantly) when compared to exporting to other file formats, like vrml, which take some time but work perfectly. Is there something I am doing wrong or an option I havent noticed to ensure export to obj file format? Thank you in advance, Vicente

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Beta-turns and hairpins
by Kyle Morris 03 Jul '12

03 Jul '12

Dear all, Is there a simple way to model beta-turns and hairpins in polypeptide chains in Chimera? Thanks in advance for any assistance, Kyle

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User Inquiry
by Yen Bui 02 Jul '12

02 Jul '12

To whom this may concern, I’m an undergraduate student doing some research at KSTATE this summer and I’ve been assigned to work on a project that utilizes Chimera. My professor is unavailable a lot of the time and I’ve been struggling a bit with a problem. I’ve been successful at opening up the following PDB files: 1DHK 1DPX 1HYL 2CAU 3BLG 1OA6 1JBC 1OA5 I’m able to open up the .pdb files, proceed to use the commands “del solvent” and “del @ .b” in the command line. I’m also able to go to ToolsàHigher Order Structure à Crystal Contacts before changing the contact distance from 1.0 to 4.0 and check mark the create copies of contacting molecules. However when I attempt to do the following actions for the rest of the proteins I run into a variety of issues: For example 2CAU: When I attempt to “measure buried area #0 # 2-7,” I get the following response in my reply log: #0, chain A: JACK BEAN vicilin 6 pairs of NCS asymmetric units of 2CAU contact at distance 1.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 1 0 4 0 0 0 0 1 1 0 5 0 0 0 0 1 1 0 6 -1 0 -1 0 1 1 0 8 0 0 0 0 1 1 0 9 0 0 -1 0 1 1 0 11 0 0 -1 0 1 C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags [End of Reply Log] So I’m not able to get back the calculations I want. Also, when I attempt to use the Surface Analysis à Attributes Calculator to run the following function : sum(atom.buriedSASArea) and check the “Restrict formula domain to current selection, if any” and “Save calculation results to file,” after selecting the “C” atoms I get the reply: Formula evaluation error: expecting vector argument in function Is there something I need to do before I attempt these actions? Also, I have very little experience with programs in general (I’m a chemistry major/upcoming experimental chemist working with theortical physicist…a little out of my element). Thanks in advance, -Yen Bui

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Alignment of symmetry axes via Chimera
by danashah＠post.tau.ac.il 02 Jul '12

02 Jul '12

Hi all, I've only joined this mailing list lately, so pardon me if this question was asked and answered before. We have two different peptides, each contains a 4-fold symmetry axis. We would like to align those two symmetry axes, without superimpose one peptide on the other, since they should be continuous. Is there a way to do that via Chimera (gui or no gui)? I was able to find this conversation: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003140.html but it doesn't solve our specific situation. Best, Dana. __ Dana Sachayni Joel Hirsch's Lab Faculty of Life Sciences Tel Aviv University Ramat Aviv, Israel e-mail: danashah(a)post.tau.ac.il

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Chimera-users July 2012