RE: [PyMOL] modifying atom coordinates
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
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 > >
RE: [PyMOL] modifying atom coordinates
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
