[Chimera-users] How to add change to multiple molecules

[Elaine Meng]

Hi Yang,
Yeung Chiu is right that you simply choose the one or more (or all)  
models from the box in Add Charge.  The lines for the models to affect  
will be highlighted, and in fact all of them were already highlighted  
when I started Add Charge in my test today.   If you click one line,  
then only that model will be chosen, but you can drag to choose a  
whole range of models, or click the first line and then Shift-click  
the last to a choose a block of lines.  Or, you can toggle each line  
between chosen and not chosen with Ctrl-click.  It doesn't matter  
which ones are displayed in the Chimera window, however.
  <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html 
 >

A separate issue is that yes, there is an "addcharge" command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>

It can also work on specified models or all models, for example
     addcharge all spec #0.1-5
     addcharge all
These would both bring up dialogs for verifying the estimated net  
charge of each nonstandard residue.  If you didn't want any dialog  
interactions (for example using Chimera in nogui mode) you would have  
to give the net charge, and in that case you can only do one residue  
type at a time.  That is probably one model in your case if each is a  
small molecule for docking:
     addcharge nonstd #0.2 -2

You can put a bunch of Chimera commands in a text file and then just  
open that file to execute it.  That is different from a shell script  
or Python script, which I believe also could be used, but I don't use  
those myself.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at 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 Nov 3, 2008, at 3:51 AM, CHIU,YEUNG wrote:

> Hi Yang
>
> You mean adding "charge"? I think you can add charge to all of the
> models as long as you check the box referred to them at the
> bottom. If you want to add charge to some models only, you can
> ~disp all, then display one by one and add charge to them. I hope
> this would help. Good luck!
>
> On Sun Nov 02 20:32:46 EST 2008, zhouyang
> <zhouyang at mail.shcnc.ac.cn> wrote:
>
>> Hi
>> Recently I wanna add change to a series of molecules for DOCK6
>> which are stored in a single .mol2 file. It seems that the
>> Chimera GUI can just add change for one molecules at one
>> operation. I wonder how to add change to all of them?
>> Alternatively I just suppose to use 'split' shell command to
>> seperate these molecules to single files and then add change to
>> them. Then the key point is whether Chimera can run in
>> command-line mode so that I can achieve by writing a shell
>> script?
>> Thanks in advance
>> Yang
>> zhouyang at mail.shcnc.ac.cn
>>
> Sincerely yours
> CHIU,YEUNG
>