[Chimera-users] how to copy partial charges from a .mol2 file to another

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 29 12:11:36 PST 2012

Hi Thomas,
If the residue and atom names are identical, it might work to open the structure with the charges, export the charge attribute to a file, close that structure and open the other one, assign the charge attribute from the file.  I don't know if that qualifies as "straightforward," however! 

How to export the attribute: start Render by Attribute (under Tools... Depiction), in that dialog choose "File... Save Attributes", specify the charge attribute of atoms, save file where you will be able to find it later.

How to read in the file to assign the attribute: start Define Attribute (under Tools... Structure Analysis), browse to the file and open it.  Remember to close the first structure and open the other one first.

There is an "mcopy" command that copies attributes from one molecule to another, but I believe it only includes stuff like color and display style, not charge.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 29, 2012, at 11:57 AM, Thomas Evangelidis wrote:

> Dear Chimera community,
> Is there any straight forward way to copy the partial charges from one .mol2 file to another?
> Thanks in advance.
> Thomas

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