On Nov 23, 2015, at 10:37 AM, Pande, Ajay K apande@albany.edu wrote:

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?

Thanks

Ajay

If you add the following two lines to the script it will print out the center of mass and dipole vector:

print “center of mass:”, com.data() print “dipole:”, dipole.data()

Make sure the lines are indented to the same level as the final print statement in the original script. With those values you can easily write a BILD format file that will draw an arrow from the center of mass to the (center of mass + dipole) and open that file to show the arrow. The BILD format is described here:

http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html

If you are doing this for many structures, it would be possible to modify the script itself to create/open the BILD file, but that would be significantly more work. But if you really need it let me know.

—Eric

From: Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> Sent: Thursday, November 19, 2015 7:56 PM To: Pande, Ajay K Cc: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@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:

http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html [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:

http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts

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

Eric Pettersen UCSF Computer Graphics Lab

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