Re: [Chimera-users] command line mode
Hi Eric, Is there some API with examples of chimera available. I am trying to add hydrogen in previous script. I tried cmdAddH and simpleAddhydrogens but it is not working. I am trying to put hydrogen and then charge to each ligand in the database. May be later I will call mmtk minimization from chimera itself to minimize each ligand. thanks in advance s
Hi S, If you enter Chimera commands, for example command: addh command: col byatom you can save them from the Command History either as the original Chimera commands or their Python translations. Open Command History (click black triangle to the right side of the command line, choose "Command History"). In the Command History, choose the lines you want to save, then click "Record..." This brings up another dialog for saving to a file. Choose the option to "Record as Python commands" and save the file. In this example, the file contains import Midas from Midas.midas_text import makeCommand makeCommand('addh') makeCommand('col byatom') The harder case is when there is no Chimera command. However, there are commands to "addh" "addcharge" and "minimize" - see their man pages for usage. http://www.cgl.ucsf.edu/chimera/current/docs/ UsersGuide/framecommand.html If you got molecules from ZINC, aren't they already in reasonable shape with hydrogens? I hope this helps, Elaine On Feb 27, 2008, at 2:16 PM, snoze pa wrote:
Hi Eric, Is there some API with examples of chimera available. I am trying to add hydrogen in previous script. I tried cmdAddH and simpleAddhydrogens but it is not working. I am trying to put hydrogen and then charge to each ligand in the database. May be later I will call mmtk minimization from chimera itself to minimize each ligand. thanks in advance s _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Feb 27, 2008, at 2:32 PM, Elaine Meng wrote:
Hi S, If you enter Chimera commands, for example command: addh command: col byatom you can save them from the Command History either as the original Chimera commands or their Python translations. Open Command History (click black triangle to the right side of the command line, choose "Command History"). In the Command History, choose the lines you want to save, then click "Record..." This brings up another dialog for saving to a file. Choose the option to "Record as Python commands" and save the file. In this example, the file contains
import Midas from Midas.midas_text import makeCommand makeCommand('addh') makeCommand('col byatom')
While the above certainly works, the preferred Python equivalent nowadays would be: from chimera import runCommand runCommand('addh') runCommand('col byatom') I have updated the Command History widget to output the "modern" equivalent now (it was my fault it didn't). It seems you figured out your hydrogen-adding and minimizing issues... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng -
Eric Pettersen -
snoze pa