Question about Coulombic electrostatic potential
Dear UCSF ChimeraX We used the ChimeraX program to calculate electrostatic potential. By using the coulombic command, a molecular surface was generated and colored. However, we also need the electrostatic potential value (kcal/(mol*e))of the protein. Could you please give some advices how to get this value? Best Regards, Sunisa Yoodee -- *Sunisa Yoodee*, Ph.D Medical Proteomics Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, THAILAND Tel: 66-8-06691102 e-mail: yd.sunisa@gmail.com
To piggy back on this question of getting more quantitative information out of ChimeraX's electrostatic/coloumbic functions, is there a way to save information about the electrostatic surface as a readable text file (or a .dx file (if that one is human readable))? I was hoping to quantitatively get a delta electrostatic surface of two surfaces at different propka-ph values. Or perhaps a way to generate that difference surface in ChimeraX? ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Sunisa Yoodee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Saturday, February 19, 2022 12:22 AM To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Question about Coulombic electrostatic potential Dear UCSF ChimeraX We used the ChimeraX program to calculate electrostatic potential. By using the coulombic command, a molecular surface was generated and colored. However, we also need the electrostatic potential value (kcal/(mol*e))of the protein. Could you please give some advices how to get this value? Best Regards, Sunisa Yoodee -- Sunisa Yoodee, Ph.D Medical Proteomics Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, THAILAND Tel: 66-8-06691102 e-mail: yd.sunisa@gmail.com<mailto:yd.sunisa@gmail.com>
Dear Sunisa, There is no single value for a protein - the electrostatic potential is a quantity that varies in 3D space, so instead of one value it is many different values on a 3D grid. Getting to Jacob's question of how to save values: ChimeraX does not yet have the option to generate a map model from the Coulombic electrostatic potential calculation. To do that, you would need to use Chimera instead. Chimera's "coulombic" command, see the last 3 options on this page: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html> ... or the GUI, Chimera menu: Tools... Structure Analysis.... Coulombic Surface Coloring, the "Compute grid..." options: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulomb...> Then in Chimera, you could save that map model to a file with the "volume" command, see saving options: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> Formats are MRC, NetCDF, BRIX, IMAGIC, or Chimera map format. I don't know if they are meant to be human-readable, you would need to investigate that further yourself. Alternatively if you just mean you want to know the value of the potential at some specific point(s) on the protein surface, see this recent post: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003337.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 19, 2022, at 6:05 AM, Anderson, Jacob via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
To piggy back on this question of getting more quantitative information out of ChimeraX's electrostatic/coloumbic functions, is there a way to save information about the electrostatic surface as a readable text file (or a .dx file (if that one is human readable))? I was hoping to quantitatively get a delta electrostatic surface of two surfaces at different propka-ph values.
Or perhaps a way to generate that difference surface in ChimeraX? From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Sunisa Yoodee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Saturday, February 19, 2022 12:22 AM To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Question about Coulombic electrostatic potential
Dear UCSF ChimeraX
We used the ChimeraX program to calculate electrostatic potential. By using the coulombic command, a molecular surface was generated and colored. However, we also need the electrostatic potential value (kcal/(mol*e))of the protein. Could you please give some advices how to get this value?
Best Regards, Sunisa Yoodee -- Sunisa Yoodee, Ph.D
Medical Proteomics Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, THAILAND Tel: 66-8-06691102 e-mail: yd.sunisa@gmail.com
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear All, Thank you so much for your suggestion. Best Regards, Sunisa Yoodee ในวันที่ จ. 21 ก.พ. 2022 เวลา 01:00 Elaine Meng <meng@cgl.ucsf.edu> เขียนว่า:
Dear Sunisa, There is no single value for a protein - the electrostatic potential is a quantity that varies in 3D space, so instead of one value it is many different values on a 3D grid.
Getting to Jacob's question of how to save values:
ChimeraX does not yet have the option to generate a map model from the Coulombic electrostatic potential calculation. To do that, you would need to use Chimera instead. Chimera's "coulombic" command, see the last 3 options on this page: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
... or the GUI, Chimera menu: Tools... Structure Analysis.... Coulombic Surface Coloring, the "Compute grid..." options: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulomb...
Then in Chimera, you could save that map model to a file with the "volume" command, see saving options: < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output
Formats are MRC, NetCDF, BRIX, IMAGIC, or Chimera map format. I don't know if they are meant to be human-readable, you would need to investigate that further yourself.
Alternatively if you just mean you want to know the value of the potential at some specific point(s) on the protein surface, see this recent post: < https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003337.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 19, 2022, at 6:05 AM, Anderson, Jacob via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
To piggy back on this question of getting more quantitative information out of ChimeraX's electrostatic/coloumbic functions, is there a way to save information about the electrostatic surface as a readable text file (or a .dx file (if that one is human readable))? I was hoping to quantitatively get a delta electrostatic surface of two surfaces at different propka-ph values.
Or perhaps a way to generate that difference surface in ChimeraX? From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Sunisa Yoodee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Saturday, February 19, 2022 12:22 AM To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Question about Coulombic electrostatic potential
Dear UCSF ChimeraX
We used the ChimeraX program to calculate electrostatic potential. By using the coulombic command, a molecular surface was generated and colored. However, we also need the electrostatic potential value (kcal/(mol*e))of the protein. Could you please give some advices how to get this value?
Best Regards, Sunisa Yoodee -- Sunisa Yoodee, Ph.D
Medical Proteomics Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, THAILAND Tel: 66-8-06691102 e-mail: yd.sunisa@gmail.com
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- *Sunisa Yoodee*, Ph.D Medical Proteomics Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, THAILAND Tel: 66-8-06691102 e-mail: yd.sunisa@gmail.com
participants (3)
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Anderson, Jacob -
Elaine Meng -
Sunisa Yoodee