Great, that seems to have fixed the problem.
Thanks for your help,
Dan
From: jason.vertr...@schrodinger.com
Date: Mon, 20 May 2013 10:25:14 -0500
Subject: Re: [PyMOL] Discrepancy between select within and distance?
To: psdny...@outlook.com
CC: pymol-users@lists.sourceforge.net
Hi,
Folmer is correct on both accounts.
First, "select" was selecting across various states into one multistate
selection. Then, the distance command was operating on the first state, which
is its default behavior. So, replace
select asdf, 1MM2////CA w. 5 of 2kgi///22/CA
with
select asdf, 1MM2////CA w. 5 of 2kgi///22/CA, state=1
or whichever state you want and try again. (Or use Folmer's suggestion of
splitting out the states.)
Second, please don't hind behind a pseudonym. We don't bite.
Cheers,
-- Jason
On Sun, May 19, 2013 at 4:55 PM, asdf asdf <psdny...@outlook.com> wrote:
Hello,
I'm measuring the distance between certain residues in an alignment and I've
noticed a discrepancy in the selections returned by the "select within command"
and the actual distances measured to the atoms returned by the selection. I
was wondering if maybe somebody knew where I was going wrong.
When I run the following commands
> fetch 1MM2
> fetch 2kgi
> align 2kgi, 1MM2
> select asdf, 1MM2////CA w. 5 of 2kgi///22/CA
> iterate asdf, print(resi + " " + resn + " " + name + " " +
> str(cmd.distance("tmp", "2kgi///22/CA", "1MM2///" + resi + "/CA")))
I get this output:
24 CYS CA 5.15101623535
25 ASP CA 3.34501266479
26 THR CA 6.03605747223
47 GLU CA 3.80576062202
48 TRP CA 3.85521435738
49 LEU CA 4.28281402588
I'm just a little confused about why atoms that are further than 5 angstroms
away from the atom I specified in the select command are returned. Is there
some difference in the way "select within" and "cmd.distance", or have a
confused some of the commands?
Any suggestions are appreciated
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--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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