[Chimera-users] surface ESP in chimera

sbasu at ffame.org sbasu at ffame.org
Thu May 29 12:59:02 PDT 2014


Dear Chimera group,

Could you please help us resolving the following issues ?

1. Is there a way to load a pre-computed solvent accessible surface (i.e.,
coordinates of dot surface points stored in a PDB format against source
atom types) on top of a protein molecule ? [kindly see the attached
example file]

2. Is there a way to print / write the actual dot surface points generated
by Chimera into a file (preferably in a PDB format with the source atom
records) ?

3. Is there a way to actually compute the electrostatic potentials (ESP)
on the solvent accessible surface by chimera using a Delphi interface ? In
that case, how can one set the delphi parameters (e.g., partial charges /
atomic radii / percentage grid fills / boundary conditions) according to
his likings ?

4. We have computed ESP on solvent accessible surface (MS - connolly)
using a standalone version of delphi. When we load the phimap.phi onto the
chimera-generated surface to obtain the ESP-colored surface map, we find
ambiguities between the surface coloring and the actual values of the
potentials (almost the entire surface is showing red / white whereas there
are obviously positive patches from the actual numbers) ! We suspect that
it is due to the inconsistency between two surfaces.

Lastly,

5. A trivial question is how to select residue(s) by residue sequence
number (e.g., 108 or 108-VAL) from the select drop-down list ? We do not
seem to find that option.

                      thanks and regards,
                      Sankar Basu
                      Post Doctoral Fellow
                      Foundation for Applied Molecular Evolution
                      Gainesville, FL 32601





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