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

[Eric Pettersen]

Hi Ajay,
	Okay I have attached a script that also shows the dipole vector as an arrow on the structure.  It will also be listed in the model panel so you can easily hide it or change its color.  If you want it to be a different length, change the setting of the “vectorScale” variable in the script itself.  The updated script is also available via the scripts page.

—Eric



> On Nov 25, 2015, at 12:11 PM, Pande, Ajay K <apande at albany.edu> wrote:
> 
> I really do need it for many structures, and I am reasonable certain many other people will too. What would be nice is that the dipole vector shows as an arrow on the pdb structure. If you can change the script file, it would be very useful.
> 
> Thanks
> 
> Ajay
> 
> 
> 
> 
> 
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Sent: Wednesday, November 25, 2015 2:50 PM
> To: Pande, Ajay K
> Cc: chimera List
> Subject: Re: [Chimera-users] calculating dipole moment of a protein in pdb
>  
> 
>> On Nov 23, 2015, at 10:37 AM, Pande, Ajay K <apande at albany.edu <mailto: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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