No, this kind of technical information isn't documented...
If I recall correctly, when PyMOL hooks fragments together, it
replaces hydrogen with a bond along the existing vectors. In other
words, one fragment is translated so as to fit onto another.
Peptides are a special case because the phi-psi vectors are
fairly well defined. Nevertheless, I wouldn't trust peptide geometries
generated by PyMOL until they've passed through some external
force-field, such as MMFF or Amber/OPLS.
PyMOL is a reasonable builder for defining the covalent scaffold
of peptides and arbitrary small molecules, but it knows nothing about
forces and energies.
Warren L. DeLano, Ph.D.
DeLano Scientific LLC
> -----Original Message-----
> From: pymol-users-admin@... [mailto:pymol-users-
> admin@...] On Behalf Of Edmund Kump
> Sent: Thursday, September 18, 2003 8:59 PM
> To: pymol-users@...
> Subject: RE: [PyMOL] modifying atom coordinates
> Yes, but what happens when, for example, I take a lysine residue, and
> connect a glutamine residue? Shouldn't all the atoms have different
> coordinates from when they are stand alone, based on the forces from
> nearby atoms? Does pymol account for this as residues are added, or is
> there a command or wizard which accounts for nearby atomic forces that
> would execute after I build my chain?
> To give some background to what I'm trying to do, the end goal of my
> project is to modify the forces involved in protien folding. I'm sorry
> I'm asking questions that are documented, but I haven't seen anything
> answers my question yet.
> Much Thanks,
> On Wed, 17 Sep 2003, Warren L. DeLano wrote:
> > Hi Edmund,
> > Actually, PyMOL uses a set of stored coordinates for fragments
> > and residues. They can be found in
> > The files have .pkl extensions, which stands for pickled chempy
> > These files can be viewed directly in PyMOL, or can be introspected
> > unpickling them in a Python interpreter.
> > Cheers,
> > Warren
> > --
> > mailto:warren@...
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax (650)-593-4020
> > > -----Original Message-----
> > > From: pymol-users-admin@... [mailto:pymol-users-
> > > admin@...] On Behalf Of Edmund Kump
> > > Sent: Wednesday, September 17, 2003 3:49 AM
> > > To: pymol-users@...
> > > Subject: [PyMOL] modifying atom coordinates
> > >
> > > Greetings,
> > >
> > > I am interested in modifying how pymol generates the coordinates
> > > atoms in a peptide chain as you add residues to it. I am an
> > > undergraduate math student, so my knowledge in this area is in the
> > > range of "nothing". I would assume that this would be in the
> > > or editor modules, but so far I haven't found what I'm looking
> > > what Chempy or Pymol module(s) can I find the code that determines
> > > these coordinates?
> > >
> > > Thanks,
> > > Edmund Kump
> > > ekump@...
> > > Applied Mathematics and Statistics
> > > SUNY Stony Brook
> > >
> > >
> > >
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