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

[Thomas Evangelidis]

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


~Thomas


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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