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

Thomas Evangelidis tevang3 at gmail.com
Wed Feb 29 13:48:41 PST 2012

Thank you Elaine for the swift reply! It was straight forward, although the
atom names were not identical and had to change them manually.


On 29 February 2012 22:11, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving
> >
> 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.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html
> >
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.html>
> 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 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
> >



Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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