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

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

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.

Tom

On Jan 10, 2017, at 7:35 AM, Sagar, Vatsala (NIH/NEI) [E] <vatsala.sagar@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@nih.gov>
Date: Friday, January 6, 2017 at 10:09 AM
To: Tom Goddard <goddard@sonic.net>, "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar@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@sonic.net>
Date: Thursday, January 5, 2017 at 7:07 PM
To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar@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

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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