[Chimera-users] dipoles

Tom Goddard goddard at sonic.net
Wed Jan 25 10:40:49 PST 2017


Hi Vatsala,

  To change the arrow thickness change the line of code in the dipole.py script

bildString = ".arrow %g %g %g %g %g %g .1 .2 .9"

The values at the end control the shape, the “.1” is the cylinder radius, the “.2” is the arrow tip cone radius, and the “.9” is the fraction of the arrow length taken by the cylinder.  This is described in the Chimera BILD format documentation here

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>

  Tom


> On Jan 25, 2017, at 10:02 AM, Sagar, Vatsala (NIH/NEI) [E]  wrote:
> 
> Hi Tom, 
> Do you know how to change the dipole vector thickness.  I am using dipole.py program to calculate dipoles in Chimera, and it is giving me a very thin line.  
> Thanks a lot,  I sincerely appreciate it,
> Vatsala Sagar
> 
> From: "Sagar, Vatsala (NIH/NEI) [F]" 
> Date: Friday, January 6, 2017 at 10:09 AM
> To: Tom Goddard , "chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" 
> Subject: Re: [Chimera-users] dipoles
> 
> Hi Tom, 
> I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another.  Please take a look at it and tell me what you think,
> Thanks,
> Vatsala
> From: Tom Goddard 
> Date: Thursday, January 5, 2017 at 7:07 PM
> To: "chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" 
> Subject: Re: [Chimera-users] dipoles
> 
> Hi Vatsala,
> 
>   I guess you are refering to the dipole.py script on the Chimera Python scripts web page:
> 
> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
> 
> Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees.  Without have the structure and rotated PQR files I don’t know what is going wrong.
> 
> Tom
> 
> 
>> On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F]  wrote:
>> 
>> Hi,
>> Do you know if there is a method to calculate dipoles in Chimera?  I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera.  I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees.  Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another.  The dipole.py scipt is calculating them as two different dipoles.  Can you help me with this?
>> Thanks,
>> Vatsala Sagar
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