coloumbic coloring when surface can't be calculated?
Hi, I have a structure (well, lots of structures) for which surface calculation fails in Chimera. I can rescue surface calculation using the ‘grid’ option (e.g. surf #0 grid 1), but then I can’t figure out how to apply coulombic coloring to that surface.
I could use APBS, but PDB2PQR seems to choke on especially large/complicated structures.
Is there any way around this? Would it be possible to export the coloumbic potential as a .dx file and use that for electrostatic surface coloring?
Cheers Oli
Hi Oli, The “coulombic” command has an “atoms” option to bypass the need for a pre-existing molecular surface. Although there are also compute-grid options to open the potential map as a volume data set, I believe you can do the coloring directly with the “coulombic” command without computing a grid, as long as the “atoms” option is used to specify the set of charged atoms independently of the surface to color. Still, it may be useful to compute a grid and then if you want to experiment with re-coloring (using Surface Color or command “scolor”), you don’t have to recompute it every time. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html
It’s been a while since I worked with the grid-type surface in Chimera, but I faintly remember it has some inconvenient idiosyncracies since it’s not explicitly tied to the atoms. ChimeraX uses this grid method of molecular surface calculation, thus avoiding the failures, and it ties (conceptually) the resulting surface to the atoms, so the behavior is better (ChimeraX doesn’t have a Coulombic calculation yet, however). Another alternative in Chimera to a standard molecular surface is to make a “molmap” surface as described in the surface-workarounds page. Coloring that surface by Coulombic ESP would be the same as described above. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html
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 Apr 29, 2017, at 12:49 PM, Oliver Clarke olibclarke@gmail.com wrote:
Hi, I have a structure (well, lots of structures) for which surface calculation fails in Chimera. I can rescue surface calculation using the ‘grid’ option (e.g. surf #0 grid 1), but then I can’t figure out how to apply coulombic coloring to that surface.
I could use APBS, but PDB2PQR seems to choke on especially large/complicated structures.
Is there any way around this? Would it be possible to export the coloumbic potential as a .dx file and use that for electrostatic surface coloring?
Cheers Oli
Thanks Elaine, that is very helpful as always!
Cheers
Oli
On Apr 29, 2017, at 8:39 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Oli, The “coulombic” command has an “atoms” option to bypass the need for a pre-existing molecular surface. Although there are also compute-grid options to open the potential map as a volume data set, I believe you can do the coloring directly with the “coulombic” command without computing a grid, as long as the “atoms” option is used to specify the set of charged atoms independently of the surface to color. Still, it may be useful to compute a grid and then if you want to experiment with re-coloring (using Surface Color or command “scolor”), you don’t have to recompute it every time. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html
It’s been a while since I worked with the grid-type surface in Chimera, but I faintly remember it has some inconvenient idiosyncracies since it’s not explicitly tied to the atoms. ChimeraX uses this grid method of molecular surface calculation, thus avoiding the failures, and it ties (conceptually) the resulting surface to the atoms, so the behavior is better (ChimeraX doesn’t have a Coulombic calculation yet, however). Another alternative in Chimera to a standard molecular surface is to make a “molmap” surface as described in the surface-workarounds page. Coloring that surface by Coulombic ESP would be the same as described above. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html
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 Apr 29, 2017, at 12:49 PM, Oliver Clarke olibclarke@gmail.com wrote:
Hi, I have a structure (well, lots of structures) for which surface calculation fails in Chimera. I can rescue surface calculation using the ‘grid’ option (e.g. surf #0 grid 1), but then I can’t figure out how to apply coulombic coloring to that surface.
I could use APBS, but PDB2PQR seems to choke on especially large/complicated structures.
Is there any way around this? Would it be possible to export the coloumbic potential as a .dx file and use that for electrostatic surface coloring?
Cheers Oli
participants (2)
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Elaine Meng -
Oliver Clarke