-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, Maybe a silly question, but I couldn't find anything in the docs. Given one structure pdb and an electrostatic potential calculated by delphi, can Chimera display the resulting dipole as a vector? Thank you very much! Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: miguel.ortiz@cnio.es - ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées
And the boring bits follow...
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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). Tom
participants (2)
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Miguel Ortiz Lombardia -
Thomas Goddard