March 2009 - Chimera-users - RBVI Mailing Lists

structure matching
by Bala subramanian 04 Mar '09

04 Mar '09

Hello all, 1) I have to superimpose two protein structures based on sequence matching say prot1 and prot2. Precisely matchmaker. My prot1 is a cryo electron microscopy structure, the structure is not continuous, it has missing residues and hence its pdb contains 3 Chains. My prot2 is a crystal structure, having one chain. I need your suggestion in superimposing these two structure wherever the sequences are matching. What i tried: I opened pro1 pdb and changed all chain names as A ( it contains chain A,B,C). Then i tried to superimpose with prot2, but matchmaker doesn work. 2) when i open molecules one by one, i need all the molecules appear in the center of the chimera window. How to set this in chimera. After opening the first pdb, when i open the second one, it is invisible. Thanks, Bala

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matchmaker output
by Karan Uppal 03 Mar '09

03 Mar '09

Hello, I want to simplify the question I asked yesterday. Is there any way to store the output of Match Maker, specifically the RMSD values for every residue and the list of residues in the alignment regions in an external file from command line? Thank you -Karan

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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

1 1

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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Chimera-users March 2009