[Chimera-users] command line mode

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 27 14:32:03 PST 2008

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('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/ 

If you got molecules from ZINC, aren't they already in reasonable  
shape with hydrogens?
I hope this helps,

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
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> Chimera-users at cgl.ucsf.edu
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