[Chimera-users] Dipole

Thomas Goddard goddard at cgl.ucsf.edu
Wed May 18 10:48:02 PDT 2005

Hi Miguel,

  I'm not sure I understand your question but I think the answer is no!

  I once saw a computer science teacher at Berkeley deliver that answer,
only the student had asked a question like "Is it better to use a linked list
or an array?" that didn't have a yes or no answer.

  Do you mean you want to know the overall dipole moment of the molecule?
In other words, what dipole electric field would be seen very far from the
molecule?  That is best calculated from the charges on the individual atoms.
The charges aren't specified in the *.phi file or the PDB file.  It would
be possible to infer the dipole moment from the electrostatic potential if
you knew it very far from the molecule, but the *.phi potential map only
gives the potential near the molecule.  I may still be possible to infer
the dipole moment from the potential near the map, but I'm not sure.
There is also the question of whether you want to account for screening
by the solvent.

  In any case, I'll stick with my answer that Chimera has no way of computing
the dipole moment.  If you had partial charges for all the atom in the
B-factor column of the PDB file (as in PQR style PDB files), it would be
relatively easy to compute the dipole moment with some python code by
summing charge times atom position (not accounting for the neutralizing
dipole produced by the solvent).  That could relatively easily be
displayed as a big arrow through the molecule by having the Python code
generate a VRML model containing an arrow (cone on top of cylinder).


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