[Chimera-users] dipoles

Tom Goddard goddard at sonic.net
Thu Jan 5 16:07:30 PST 2017

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.


> 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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