Re: [Chimera-users] dipoles
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 <mailto:vatsala.sagar@nih.gov>> Date: Friday, January 6, 2017 at 10:27 AM To: "chimera-bugs@cgl.ucsf.edu <mailto:chimera-bugs@cgl.ucsf.edu>" <chimera-bugs@cgl.ucsf.edu <mailto:chimera-bugs@cgl.ucsf.edu>> Subject: FW: [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 <mailto:goddard@sonic.net>> Date: Thursday, January 5, 2017 at 7:07 PM To: "chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar@nih.gov <mailto: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 <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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html> 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 ---------- 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@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
participants (2)
-
Elaine Meng -
Sagar, Vatsala (NIH/NEI) [E]