ChimeraX - Color by Electrostatic Potential
Hi,
is there a way to color the protein surface according to Electrostatic Potential, just like we do with Chimera ("Electrostatic Surface coloring" under "Tools"). The input potential file was calculated with Delphi.
Thanks in advance, Maurício Menegatti Rigo, *Ph.D.* Brazil
Hi Maurício, Yes, with the ChimeraX color command, for example something like:
color electrostatic #1 map #2 palette -10,red:0,white:10,blue
…where the protein with surface is #1 and the DelPhi map is #2.
There are other possible options, see: http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map
You can open the DelPhi file in all the usual ways (File… Open or “open” command). We read the .phi files from the academic version. Here are the known map types: http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume
When you open the map it may show isosurfaces, which you can hide by clicking the “eye” icon near the upper left corner of the Volume Viewer panel. http://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.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 Sep 14, 2018, at 10:26 AM, Maurício Menegatti Rigo mauriciomr1985@gmail.com wrote:
Hi, is there a way to color the protein surface according to Electrostatic Potential, just like we do with Chimera ("Electrostatic Surface coloring" under "Tools"). The input potential file was calculated with Delphi. Thanks in advance, Maurício Menegatti Rigo, Ph.D. Brazil
Got it! Thank you so much for your help!
Best, Maurício Menegatti Rigo
Em sex, 14 de set de 2018 às 14:55, Elaine Meng meng@cgl.ucsf.edu escreveu:
Hi Maurício, Yes, with the ChimeraX color command, for example something like:
color electrostatic #1 map #2 palette -10,red:0,white:10,blue
…where the protein with surface is #1 and the DelPhi map is #2.
There are other possible options, see: http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map
You can open the DelPhi file in all the usual ways (File… Open or “open” command). We read the .phi files from the academic version. Here are the known map types: http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume
When you open the map it may show isosurfaces, which you can hide by clicking the “eye” icon near the upper left corner of the Volume Viewer panel. http://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.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 Sep 14, 2018, at 10:26 AM, Maurício Menegatti Rigo <
mauriciomr1985@gmail.com> wrote:
Hi, is there a way to color the protein surface according to Electrostatic
Potential, just like we do with Chimera ("Electrostatic Surface coloring" under "Tools"). The input potential file was calculated with Delphi.
Thanks in advance, Maurício Menegatti Rigo, Ph.D. Brazil
participants (2)
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Elaine Meng -
Maurício Menegatti Rigo