[Chimera-users] dipoles

Tom Goddard goddard at sonic.net
Tue Jan 10 10:30:53 PST 2017

Hi Vatsala,

  If you run the Chimera pdb2pqr command or graphical interface on a molecule and a rotated copy of the same molecule and it gives different protonation states for histidine that seems like a bug.  As described in the Chimera documentation this uses the PDB2PQR web service provided by the  National Biomedical Computation Resource (NBCR).

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html>

You might want to contact the developers of PDB2PQR to pursue this matter further

	http://www.poissonboltzmann.org/support/home/ <http://www.poissonboltzmann.org/support/home/>

Chimera can also add hydrogens and compute charges using the Chimera DockPrep tool so maybe that is an option for you to avoid this problem in pdb2pqr.


> On Jan 10, 2017, at 7:35 AM, Sagar, Vatsala (NIH/NEI) [E] <vatsala.sagar at nih.gov> wrote:
> Hi Tom, 
> So if you align the pdb files of the rotated proteins, they have an exact match.  But when you make the PQR files, it adds hydrogens differently to the rotated proteins, resulting in a charge difference in the said histidine.  Should the program be adding  hydrogens differently to the rotated proteins, and is there a way to remedy this>
> Thanks a lot,
> Vatsala Sagar
> From: "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar at nih.gov <mailto:vatsala.sagar at nih.gov>>
> Date: Friday, January 6, 2017 at 10:09 AM
> To: Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>, "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]" <vatsala.sagar at nih.gov <mailto:vatsala.sagar at nih.gov>>
> 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 <goddard at sonic.net <mailto:goddard at sonic.net>>
> 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]" <vatsala.sagar at nih.gov <mailto:vatsala.sagar at nih.gov>>
> 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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