[Chimera-users] dipoles

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 12 12:09:36 PST 2017

Hi Vatsala,
If you are using PDB2PQR to add the hydrogens, it is done by a web service running a separate program.  In other words, it wouldn’t be under our control of how it works, it is outside of Chimera.  Description here:

You could try instead adding the hydrogens first with Chimera, and then running PDB2PQR after that.  In that case, it might not have a different result. 

However, you’d have to try it to be absolutely sure.  Sometimes there are small changes due to coordinates rounding when some structure is moved or rotated that might possibly cause a different result of some calculation.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 10, 2017, at 7:34 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

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