RE: [PyMOL] modifying atom coordinates

[Edmund K. <ek...@ma...>]

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:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax   (650)-593-4020
>
> > -----Original Message-----
> > From: pym...@li... [mailto:pymol-users-
> > ad...@li...] On Behalf Of Edmund Kump
> > Sent: Wednesday, September 17, 2003 3:49 AM
> > To: pym...@li...
> > 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...@ma...
> > Applied Mathematics and Statistics
> > SUNY Stony Brook
> >
> >
> >
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