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

Eric Pettersen pett at cgl.ucsf.edu
Wed Nov 25 11:50:24 PST 2015


> On Nov 23, 2015, at 10:37 AM, Pande, Ajay K <apande at 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 at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>
> Sent: Thursday, November 19, 2015 7:56 PM
> To: Pande, Ajay K
> Cc: Chimera-users at cgl.ucsf.edu <mailto: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:
> 
> 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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