Elaine and co, I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this: select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number. Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher. Thank you for your excellent program and support. Ed ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole brignole@scripps.edu 443-653-2070 (cell) 858-784-8598 (lab)
Hi Ed, The "write" command only allows you to save one model at a time. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> To save multiple models to one PDB file you have to use the GUI ("File... Save PDB" or "Actions... Write PDB"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote:
Elaine and co,
I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this:
select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select
The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number.
Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher.
Thank you for your excellent program and support.
Ed
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole
brignole@scripps.edu 443-653-2070 (cell) 858-784-8598 (lab)
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Other possibilities include using the "combine" command to combine models 6, 8, and 9 into a single model (with model 0 as the 'refMol') and then use the write command on that (omitting 'relative 0'), or writing the models to separate files and using 'system cat file1 file2 file3 > file4' to combine them (though there would be END records between the models that way). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 1, 2009, at 1:11 PM, Elaine Meng wrote:
Hi Ed, The "write" command only allows you to save one model at a time. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
To save multiple models to one PDB file you have to use the GUI ("File... Save PDB" or "Actions... Write PDB"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote:
Elaine and co,
I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this:
select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select
The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number.
Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher.
Thank you for your excellent program and support.
Ed
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole
brignole@scripps.edu 443-653-2070 (cell) 858-784-8598 (lab)
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Great suggestion, I'll just use cat and strip the END lines. Since I want to then use these with morph conformations will I also have to resequence the atom id's? Ed ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole brignole@scripps.edu 443-653-2070 (cell) 858-784-8598 (lab) -----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Wed 4/1/2009 1:26 PM To: Edward Brignole Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] write selected command Other possibilities include using the "combine" command to combine models 6, 8, and 9 into a single model (with model 0 as the 'refMol') and then use the write command on that (omitting 'relative 0'), or writing the models to separate files and using 'system cat file1 file2 file3 > file4' to combine them (though there would be END records between the models that way). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 1, 2009, at 1:11 PM, Elaine Meng wrote:
Hi Ed, The "write" command only allows you to save one model at a time. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
To save multiple models to one PDB file you have to use the GUI ("File... Save PDB" or "Actions... Write PDB"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote:
Elaine and co,
I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this:
select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select
The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number.
Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher.
Thank you for your excellent program and support.
Ed
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole
brignole@scripps.edu 443-653-2070 (cell) 858-784-8598 (lab)
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Ed, If the purpose of the combination is to use Morph Conformations, then I think you're in for a world of hurt unless you use the 'combine' method. One problem with the 'cat' method is the serial numbers as you surmised. If you have any non-standard residues that require CONECT records then the serial numbers will be a real issue. Another problem is that if you have any chains in models 8 and 9 that duplicate the ones you're using from #6 (a-p) or duplicate each other then Morph Conformations will probably fall over. 'combine' will rename chains that are in conflict and renumber problem residues. 'write' with the combined model will produce unique serial numbers. So your previous commands: select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select could instead be: sel #6:.a-p sel invert sel del sel combine #6,8,9 refMol 0 modelId 7 write #7 /path/to/file.pdb BTW, you have to use a daily build to get the 'modelId' part of the 'combine' command. If your models #8 and 9 are just small molecules then you may be able to get away with the 'cat' method by stripping CONECT records in addition to END records -- making Chimera come up with the connectivity itself (though if the residues had the same number and chain ID as other residues...). --Eric On Apr 1, 2009, at 1:32 PM, Edward Brignole wrote:
Great suggestion, I'll just use cat and strip the END lines. Since I want to then use these with morph conformations will I also have to resequence the atom id's?
Ed
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole
brignole@scripps.edu 443-653-2070 (cell) 858-784-8598 (lab)
-----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Wed 4/1/2009 1:26 PM To: Edward Brignole Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] write selected command
Other possibilities include using the "combine" command to combine models 6, 8, and 9 into a single model (with model 0 as the 'refMol') and then use the write command on that (omitting 'relative 0'), or writing the models to separate files and using 'system cat file1 file2 file3 > file4' to combine them (though there would be END records between the models that way).
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Apr 1, 2009, at 1:11 PM, Elaine Meng wrote:
Hi Ed, The "write" command only allows you to save one model at a time. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
To save multiple models to one PDB file you have to use the GUI ("File... Save PDB" or "Actions... Write PDB"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote:
Elaine and co,
I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this:
select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select
The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number.
Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher.
Thank you for your excellent program and support.
Ed
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole
brignole@scripps.edu 443-653-2070 (cell) 858-784-8598 (lab)
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Edward Brignole -
Elaine Meng -
Eric Pettersen