[Chimera-users] Calculting protein dipole moment

[Boaz Shaanan]

Thanks Elaine, it works for me too with the dipole.py script.

Cheers,

         Boaz



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710





________________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, April 4, 2019 7:16 PM
To: בעז שאנן
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Calculting protein dipole moment

Hi Boaz,
Yes, Chimera reads PQR files and assigns the atom attributes “charge” (used by the script, I believe) and “radius" from the corresponding columns.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#PQR>

I tried an example just now.  It works with either the .pqr or .pdb filename suffixes.  Tested by opening the file, starting Render by Attribute, and showing the histogram for atom attribute “charge.”
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 3, 2019, at 6:31 PM, Boaz Shaanan <bshaanan at bgu.ac.il> wrote:
>
> Hi,
> Is it possible to read a .pqr file from pdb2pqr to the script for calculating dipole moment (from the chimera repository) rather than running addcharge?
> Thanks,
> Boaz