Edmund, 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. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Edmund Kump > Sent: Thursday, September 18, 2003 8:59 PM > To: pymol-users@lists.sourceforge.net > 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 I > 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 if > I'm asking questions that are documented, but I haven't seen anything that > answers my question yet. > > Much Thanks, > Edmund > > > 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 $PYMOL_PATH/data/chempy/fragments. > > The files have .pkl extensions, which stands for pickled chempy model. > > These files can be viewed directly in PyMOL, or can be introspected by > > unpickling them in a Python interpreter. > > > > Cheers, > > Warren > > > > -- > > mailto:war...@delanoscientific.com > > Warren L. DeLano, Ph.D. > > Principal Scientist > > DeLano Scientific LLC > > Voice (650)-346-1154 > > Fax (650)-593-4020 > > > > > -----Original Message----- > > > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > > > ad...@lists.sourceforge.net] On Behalf Of Edmund Kump > > > Sent: Wednesday, September 17, 2003 3:49 AM > > > To: pymol-users@lists.sourceforge.net > > > Subject: [PyMOL] modifying atom coordinates > > > > > > Greetings, > > > > > > I am interested in modifying how pymol generates the coordinates of > > > 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 bonding > > > or editor modules, but so far I haven't found what I'm looking for. In > > > what Chempy or Pymol module(s) can I find the code that determines > > > these coordinates? > > > > > > Thanks, > > > Edmund Kump > > > ek...@mathlab.sunysb.edu > > > Applied Mathematics and Statistics > > > SUNY Stony Brook > > > > > > > > > > > > ------------------------------------------------------- > > > This sf.net email is sponsored by:ThinkGeek > > > Welcome to geek heaven. > > > http://thinkgeek.com/sf > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users