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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