- Chimera-users - RBVI Mailing Lists

Programming within Chimera
by Mario Dejung 10 Jul '12

10 Jul '12

Hi all, is there an easy way to test and develop programs within Chimera? I always write python scripts and open these in Chimera… Would be much easier to have something like idle or similar to develop scripts and test them. Or is there a better way I did not found? Looking forward to any suggestions. Kind regards Mario

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(no subject)
by Khalil Raja Howard 10 Jul '12

10 Jul '12

Vv bb n8bv. Mvv vtbv t. B b7bn. B'v vb v v 7iv vt. B bv Sent from my Samsung Epic™ 4G Touch

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chimera1.6.1 model panel
by MARY VARUGHESE 10 Jul '12

10 Jul '12

Hi, I have installed the chimera1.6.1 in ubuntu 64 bit. Installation successful. But in the model panel tool only the 'activate all' button is working. although added to the favourite list all other function buttons are not working. Do anyone know how to sort out this problem. Also do anyone know the correct usage of savesphgen command when used in the command line tool of chimera. Thanking you Mary Varughese

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Android download
by Frank Irby 09 Jul '12

09 Jul '12

Hello I love using chimera I just upgraded my mac to 10.5.8. But I can't get past the python script for downloading chimera-1.6.2-mac.dmg I agree to the terms of use..... If you could email me a download link... That would be awsome.. Thanks Frank http://mandelscape.deviantart.com/gallery/ http://dreamscape.myartsonline.com/ Sent from Yahoo! Mail on Android

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AMBER99SB
by Nikolay Igorovich Rodionov 09 Jul '12

09 Jul '12

Hi all, I just have a quick question. Is AMBER99SB a fixed charge or polarizable forcefield? Thank you, Nikolay Rodionov

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Raytracing with clip planes
by Tom Goddard 09 Jul '12

09 Jul '12

Hi Ed, File / Save Image... with raytracing enabled correctly handles both the near clip plane and per-model clip planes in Chimera 1.6.1 and 1.6.2. Probably you are using an older Chimera release. I know at some point in the past the raytraced image saving did not handle clip planes. Tom > Hi, > When I use POV ray tracing in Chimera, it appears to ignore a > clipping plane (the rendered image is unclipped). Is there any way > around this? > Regards, > Ed

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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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