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@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, April 4, 2019 7:16 PM To: בעז שאנן Cc: chimera-users@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@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