RE: [PyMOL] Calpha-Calpha distance

[DeLano, W. <wa...@su...>]

PyMOL is currently just a little too smart in this area -- it checks to =
see whether the CA atoms are connected through C and N atoms.  The next =
version will support CA traces with just CA positions.=20

In the meantime, you might want to look into the CGO capability, which =
lets you draw arbitrary kinds of graphics without this kind of trickery.

- Warren

PS. Here is one of the examples "cgo01.py" included with PyMOL: "run =
cgo01.py"

# this is a trivial example of creating a cgo object consisting of a
# a single state=20

from pymol.cgo import *
from pymol import cmd

# first we create a list of floats containing a GL rendering stream

obj =3D [
   BEGIN, LINES,
   COLOR, 1.0, 1.0, 1.0,
  =20
   VERTEX, 0.0, 0.0, 0.0,
   VERTEX, 1.0, 0.0, 0.0,
  =20
   VERTEX, 0.0, 0.0, 0.0,
   VERTEX, 0.0, 2.0, 0.0,
  =20
   VERTEX, 0.0, 0.0, 0.0,
   VERTEX, 00, 0.0, 3.0,

   END
   ]

# then we load it into PyMOL

cmd.load_cgo(obj,'cgo01')

# move the read clipping plane back a bit=20

cmd.clip('far',-5)

> -----Original Message-----
> From: Daniel John Rigden [mailto:da...@ce...]
> Sent: Wednesday, October 23, 2002 10:54 AM
> To: pym...@li...
> Subject: [PyMOL] Calpha-Calpha distance
>=20
>=20
> Hi all
>=20
> I have a PDB file which uses a series of pseudo-Calpha=20
> positions to draw
> an arrow.  The positions are 3.0A apart.  This is OK for them=20
> to be joined
> in a Calpha trace made in, for example, O and RASMOL, but=20
> PYMOL must have
> a more stringent cutoff.  I've had a look but I can't see how=20
> to change
> this, or even if that's possible.
>=20
> Thanks for your help.
>=20
> Daniel
>=20
>=20
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