- Chimera-users - RBVI Mailing Lists

Web Access Data
by Thiruvarangan Ramaraj 03 Mar '09

03 Mar '09

Hello All, I created a session and saved it under .chimerax extension. I have a link to this session on a web page. When I click on this link I wanted the session to open directly using the chimera program. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… I tried to follow the instructions given in the above link, still I am unsuccessful in figuring it out. Any suggestions/ideas would be greatly appreciated. Thank You Thiru

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save image with --nogui
by Mark Moll 03 Mar '09

03 Mar '09

I'd like to load some pdb files, change the view/colors/representation/ etc., and save the resulting view as an image. If possible, I'd like to do this in the background without the GUI. This doesn't seem to work. The latest daily build gives the errors below when using this simple script: import Midas Midas.copy(file='test.png', format='PNG', width=600, height=400) Should I be using a different command? > /Applications/Chimera.app/Contents/MacOS/chimera --nogui foo.pdb test.py Opening foo.pdb... Executing test.py...Rendering high resolution image... Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/ __main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/chimeraInit.py", line 420, in init chimera.openModels.open(a, prefixableType=1) File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/chimera/__init__.py", line 1368, in open File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/chimera/__init__.py", line 802, in _openPython File "test.py", line 10, in <module> Midas.copy(file='test.png', format='PNG', width=600, height=400) File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/Midas/__init__.py", line 1049, in copy File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/chimera/printer.py", line 1176, in saveImage AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' Error while processing test.py: AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' (see reply log for Python traceback info) -- Mark

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Saving MultAlign Viewer header information using python
by Karan Uppal 02 Mar '09

02 Mar '09

Hello, I am trying to write a Python script to extract the header information from the MultAlign Viewer tool. Are there any command-line commands to interface with this tool and save the header information without manually using the toolbar. Thank you -Karan Uppal

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finding salt bridges
by Elaine Meng 28 Feb '09

28 Feb '09

> Hi everybody, I just realized my previous suggestion would not include the positively charged histidines, and I have not been able to think of a selector for just those nitrogens. > Example commands to first select by atom type and then find the H- > bonds: > > sel O2- | O3- | N3+ | Ng+ > findhbond selRestrict both saveFile ~/mydir/myfile Sorry about that, 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

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Reverse of AddH
by Francesco Pietra 27 Feb '09

27 Feb '09

Hi: Is it possible to remove all hydrogens by command, without intervening manually on the pdb file? I have to rmsd the starting (no H) pdb with the final structure after MD (with H). AddH command to the starting structure would place H not optimized, while MD has also changed the C-backbone conformation. Thanks francesco pietra

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solvent accessible area
by Bala subramanian 27 Feb '09

27 Feb '09

chimerians, I want to calculate the solvent accessible surface area for each atom and write it in the pdb file, kindly tell me how to do it. This is something i used to do with GRASP. it calculates the sasa for each atom and it can be written as a pdb file with sasa in the last column. Thanks, hve nice weekend Bala

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solvent accessible area
by Boaz Shaanan 27 Feb '09

27 Feb '09

Hi Bala, The program areaimol in the ccp4 package will do just that (i.e. generate a pdb file with the sasa value in the b-factor column). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Multiscale model of RNAP : fibrous aspect
by Damien Larivière 27 Feb '09

27 Feb '09

Dear Elaine, I used the Multiscale Model tool to create a low resolution surface of the PDB 1L9U (TAQ RNA polymerase). The attached image is what I got with a resolution 4 : a fibrous structure. So, I wonder what such a fibrous aspect means or whether it means the tool has some difficulties to create the surface with this specific protein ? Thanks for your help Damien

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How to refer to Chimera in a Newsletter
by Gary Newton 26 Feb '09

26 Feb '09

Hello... I am writing a newsletter for the SER-CAT synchrotron beamlines sector 22 at APS - the newsletter is called the "SER-CAT Spectrum" and is distributed primarily to beamline users. I have included a simple protein drawing produced by CHIMERA and indicated that the drawing was produced by CHIMERA. Should I include a trademark symbol or perhaps a copyright symbol after the name? Thanks for any advice. Best, Gary Newton University of Georgia Athens, GA

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searching chimera archieve
by Bala subramanian 26 Feb '09

26 Feb '09

Dear Elaine, Long time back, I posted a question on *searching chimera archive for a keyword*. Just for an example, i gave "salt bridge" as a key word in the following link, but it dose nt show me the queries on salt bridge in chimera archive. I dnt undertand why ?. It would helpful for chimera loves like me not to repeat same queries and also to understand all ways of analyzing salt bridge based on previous queries. I am sorry if this question is not relevant to chimera technical issues. http://www.cgl.ucsf.edu/chimera/docs/feedback.html Cheers, Bala

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