Hi,
I wonder if there is any way to list atoms an atom is bonded to? I would like
to list H bonded pairs but the available scritps (list_hbonds.py, or
polarpairs.py) only check for distance and angle between heteroatoms, but not
if any of them is actually connected to a hydrogen. As a result tw
noe_regex pattern so that it is
recognised?
Thanks in advance,
regards,
Krisztina
--- On Mon, 10/29/12, Thomas Holder wrote:
From: Thomas Holder
Subject: Re: [PyMOL] visualise NOEs
To: "Krisztina Feher" , "pymol-users"
Date: Monday, October 29, 2012, 4:23 PM
Hi Krisztina,
s,
Krisztina
ps. If this script works for on your
system, please write me too!
--- On Sun, 10/28/12, Krisztina Feher wrote:
From: Krisztina Feher
Subject: [PyMOL] visualise NOEs
To: pymol-users@lists.sourceforge.net
Date: Sunday, October 28, 2012, 10:14 PM
Hi,
I am looking for a script that
Hi,
I am looking for a script that could show CNS type distance restraints on a pdb
structure. In fact I have found a script on Justin Lorieau's homepage
(http://www.lorieau.com/software/biophysics-software/40-plot-xplor-noes-in-pymol.html)
that seems to intend to do exactly what I want, but it
Hi,
I have two chemically identical molecules, but with different residue names,
residue numbers and atom numbers. However the atom coordinates are also
different. Is there some script that could map down the atom names, residue
names and numbers to each other?
Thanks for any ideas!
Krisztina
a script on the PyMOLWiki which provides that:
http://pymolwiki.org/index.php/Get_raw_distances
cmd.distance('tmp', 'hcpl1' ,'hcpl2', 5.0)
for (i1, i2, dst) in get_raw_distances('tmp'):
f.write("%8.3f\n" % dst)
Hope that helps.
Cheers,
Thomas
Hi Everyone,
I would like to write a script, which writes out intermolecular distances
shorter than 5A between hydrogens into a text file. Here is what I made so far
on the basis of the Measure distance script in the respository:
from pymol import cmd
# open dist.txt for writing
f=open('dist.t
