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
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 Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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 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
Your structures are rotated 180 degrees relative to one another, not 90 degrees. And the charge is not the same of the two copies, HIS 53 has different charges. Removing HIS 53 (del :53) gives exactly opposite dipole vectors as expected. Tom
On Jan 6, 2017, at 7:09 AM, Sagar, Vatsala (NIH/NEI) [F] wrote:
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 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]" 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>
<0.15_80_10_pH6.5_hgd.result.pdb><0.15_80_10_pH6.5_hgd2.result.pdb><hgd.pdb><hgd2.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Sagar, Vatsala (NIH/NEI) [F] -
Tom Goddard