[Chimera-users] Setting selection mode command line

rswett at chem.wayne.edu rswett at chem.wayne.edu
Mon Dec 16 11:44:51 PST 2013

Alright, thanks.
I was hoping to be able to manipulate some excessively large pdb files  
using chimera commandline only with the --nogui option to get around  
the display problem. I had intended to open three files, one protein,  
one solvated system and one standalone ligand. Align the protein to  
the solvated system and use the zone selection to carve out a sphere  
around the standalone ligand, saving that portion of the solvated  
system and the entirety of both progtein structures into a single  
file. If you have any suggestions let me know. I'll start looking int  
aliasing if you think that would help bet around the gui.

As it stands, I can't get it to work with the --nogui flag on windows  
anyway. I'm using the command
chimera --nogui block.cmd
where block.cmd simply opens the solvated system and ligand, selects a  
zone around the ligand and saves the selected atoms to a file, but I  
get no output and it runs too fast to be actually reading in the  
structures. Suggestions? I'm using the 1.8.1 build

Quoting Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Rebecca,
> As far as I know, you cannot change the selection mode in a command.  
>  However, with commands you can often circumvent selection entirely,  
> or in the few cases where you can't easily do that (for example, the  
> "findhbond" command uses selections), there are sometimes  
> alternative routes to achieving the same result.   In the command  
> line, you can make a selection and then use ~select to deselect only  
> part of it.  Sometimes instead of selections you can use aliases and  
> combinations of aliases.  For writing a subset of the coordinates,  
> you could undisplay the unwanted atoms and use the corresponding  
> option to the "write" command to exclude them from the output.  Or,  
> depending on exactly what you are doing, you could just delete the  
> unwanted atoms before saving to a file.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
> Avoiding selection may be one of the advantages of commands, since  
> (as you found) drawing the selection outlines can make things slow.
> 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 Dec 16, 2013, at 8:13 AM, rswett at chem.wayne.edu wrote:
>> Hi all,
>> I'm interested in putting together a script that will open several  
>> large pdb files, select some very specific pieces of those files  
>> and save the output to another file. The problem is that they are  
>> large files and unwieldy in a graphics window. I have no problem  
>> generating the commands to select the regions I'm interested in,  
>> but I still need to be able to switch selection modes in between  
>> commands. Is there a way to change the selection mode at the  
>> command line without navigating the selection menu?
>> Rebecca

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