how to run the command line chimera without actually opening the GUI
Hello, I have two structures to superimpose using the match command in chimera. Once the structures are matched, I save the two models in one pdb file. I can then just view this pdb file whenever I want. My question is: can I somehow just do this using the terminal? Meaning the graphic of chimera doesn't launch, but I get the pdb file that has the correct rotation matrix of the two superimposed structures. I don't have much programming experience, and I have no knowledge of calculating rmsd. Would appreciate if someone would pinpoint me where to start. Thanks.
Hi Nurul, I think you can just use Chimera in nogui mode with a Chimera command file as input. No programming is needed if there are commands to do what you want. In this case, it sounds like the commands "open" (to open the input PDB files), "match" (or maybe instead "matchmaker"?) and "write" will do what you need. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> First figure out the exact commands you would need, then put them in a plain text file, which is the Chimera command file. If you just tried the commands by typing them in Chimera the regular way, you can save them to a text file from the Command History. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/history.html>
From terminal, you would run Chimera with the --nogui startup option and specify the command file as input. Details on that: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html>
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 Oct 20, 2011, at 2:05 AM, nurul wrote:
Hello, I have two structures to superimpose using the match command in chimera. Once the structures are matched, I save the two models in one pdb file. I can then just view this pdb file whenever I want. My question is: can I somehow just do this using the terminal? Meaning the graphic of chimera doesn't launch, but I get the pdb file that has the correct rotation matrix of the two superimposed structures. I don't have much programming experience, and I have no knowledge of calculating rmsd. Would appreciate if someone would pinpoint me where to start. Thanks.
Hi Nurul, Here's a specific example chimera --nogui --silent 3h47.pdb 1e6j.pdb align.cmd which produces a file called "aligned.pdb" which is a copy of 3h47.pdb such that it is aligned with 1e6j.pdb. The --nogui option says not to show any windows, and --silent says not to show log messages. I ran this command in a directory containing 3 files 3h47.pdb, 1e6j.pdb and align.cmd. The align.cmd file contains two lines mmaker #1 #0 write relative #1 #0 aligned.pdb These align model #1 to #0 using best matching chains (mmaker command), and write the result. Here are two problems. 1) The Chimera command script always writes the same file "aligned.pdb". There is no way I could see to specify the output file name in the command or have it write "aligned_3h47.pdb", or any other name that depends on the input files. 2) You asked that both the aligned model and reference model are written to one PDB file. The Chimera "write" command can only write one model to a PDB file (although a Chimera dialog can write both). Tom -------- Original Message -------- Subject: Re: [Chimera-users] how to run the command line chimera without actually opening the GUI From: Elaine Meng To: nurul Date: 10/20/11 8:47 AM
Hi Nurul, I think you can just use Chimera in nogui mode with a Chimera command file as input. No programming is needed if there are commands to do what you want. In this case, it sounds like the commands "open" (to open the input PDB files), "match" (or maybe instead "matchmaker"?) and "write" will do what you need.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
First figure out the exact commands you would need, then put them in a plain text file, which is the Chimera command file. If you just tried the commands by typing them in Chimera the regular way, you can save them to a text file from the Command History.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/history.html>
From terminal, you would run Chimera with the --nogui startup option and specify the command file as input. Details on that: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html>
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 Oct 20, 2011, at 2:05 AM, nurul wrote:
Hello, I have two structures to superimpose using the match command in chimera. Once the structures are matched, I save the two models in one pdb file. I can then just view this pdb file whenever I want. My question is: can I somehow just do this using the terminal? Meaning the graphic of chimera doesn't launch, but I get the pdb file that has the correct rotation matrix of the two superimposed structures. I don't have much programming experience, and I have no knowledge of calculating rmsd. Would appreciate if someone would pinpoint me where to start. Thanks.
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On Oct 20, 2011, at 11:46 AM, Tom Goddard wrote:
Here are two problems. 1) The Chimera command script always writes the same file "aligned.pdb". There is no way I could see to specify the output file name in the command or have it write "aligned_3h47.pdb", or any other name that depends on the input files.
That's true, though typically after the "chimera --nogui ..." command you when then just do "mv aligned.pdb bettername.pdb" using whatever scripting magic your shell supports.
2) You asked that both the aligned model and reference model are written to one PDB file. The Chimera "write" command can only write one model to a PDB file (although a Chimera dialog can write both).
Right. Might get improved someday. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (4)
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Elaine Meng -
Eric Pettersen -
nurul -
Tom Goddard