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.
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
from pymol.cgo import *
from pymol import cmd
# first we create a list of floats containing a GL rendering stream
obj = [
BEGIN, LINES,
COLOR, 1.0, 1.0, 1.0,
VERTEX, 0.0, 0.0, 0.0,
VERTEX, 1.0, 0.0, 0.0,
VERTEX, 0.0, 0.0, 0.0,
VERTEX, 0.0, 2.0, 0.0,
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
cmd.clip('far',-5)
> -----Original Message-----
> From: Daniel John Rigden [mailto:dan...@cenargen.embrapa.br]
> Sent: Wednesday, October 23, 2002 10:54 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Calpha-Calpha distance
>
>
> Hi all
>
> I have a PDB file which uses a series of pseudo-Calpha
> positions to draw
> an arrow. The positions are 3.0A apart. This is OK for them
> to be joined
> in a Calpha trace made in, for example, O and RASMOL, but
> PYMOL must have
> a more stringent cutoff. I've had a look but I can't see how
> to change
> this, or even if that's possible.
>
> Thanks for your help.
>
> Daniel
>
>
> +-------------------------------------------------------------
> ------------+
> | Dr Daniel John Rigden
> |
> | CENARGEN/EMBRAPA | e-mail:
> dan...@cenargen.embrapa.br |
> | Parque Estacao Biologica |
> http://www.cenargen.embrapa.br |
> | PqEB - Final - Av. W3 Norte | Phone: +55
> (61)448-4741 |
> | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55
> (61)340-3658 |
> +-------------------------------------------------------------
> ------------+
>
>
>
>
>
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