Dear pymol users,
I would like to obtain with Pymol (v1.3) the number of urea molecules in the
first shell of a peptide. To do this I have defined the object urea as
following
select UREA, resn URE
and used the following cutoff for the first hydration shell:
select UREA_firstshell, UREA
for the pymol-users mailing list archive and to close my message
Tsjerk Wassenaar gave the command :
print cmd.count_atoms(byres resn URE within 3.5 of peptide)/8. it works !!!
Thanks to him !!!
Bye
Stephane
--
Message: 8
Date: Fri, 28 Sep 2012 12:59:27 +
Hi Stephane,
Tsjerk as usual provides a clever answer. However, if in any case a
urea goes missing an atom, maybe due to experimental reasons, or you
want to use this technique for something other than urea then Tsjerk's
answer will need to be modified.
I offer a slightly different solution.
print len(set([(i.resn, i.resi) for i in cmd.get_model(resn URE).atom])) # :-)
Cheers,
Tsjerk
On Fri, Sep 28, 2012 at 4:37 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Stephane,
Tsjerk as usual provides a clever answer. However, if in any case a
urea goes missing an atom,
Works perfectly. I see no difference with no setting defer_builds_mode --
only that the movie eats no memory and works blazingly fast.
Thank You.
On Sat, Jun 23, 2012 at 11:07 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Boris,
Sorry to be nearly a month late on this, but
Last week I tried the latest svn -- the problem is still there. Why not
push Holder's solution to the latest svn?
I'm using pymol 1.5.0.3 with a Thomas Holder's solution to include VMD
plugins.
On Wed, May 30, 2012 at 7:10 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Greetings,
