[Chimera-users] calculating dipole moment of a protein in pdb

Pande, Ajay K apande at albany.edu
Mon Nov 23 10:37:44 PST 2015

Hi Eric,

It does give me the numerical value of the dipole moment, but how do I generate the dipole vector in the pdb structure?



From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Thursday, November 19, 2015 7:56 PM
To: Pande, Ajay K
Cc: Chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] calculating dipole moment of a protein in pdb

Hi Ajay,
The script referenced in this chimera-users archive message will compute it:

[Chimera-users] BCC CHARGES
I've attached a script that if you run it (File->Open, or "open ~/ dipole.py" [if it's in your home directory]) will print the dipole moments of all open molecular ...
Read more...<http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html>

Extracting the script from that message may be challenging, so I'm attaching it again.  It's also available from our Chimera Scripts page:


Like it says in the original message you have to assign partial charges before running the script (Tools->Structure Editing->AddCharge, or the "addcharge" command).


Eric Pettersen
UCSF Computer Graphics Lab

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