Hi,
I thinks this is the expected behaviour
2013/5/19 asdf asdf <psdny...@outlook.com>
> 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
>
You do not specify what state (http://pymolwiki.org/index.php/State) you
want to look at, so the selection takes in any atoms that are within the
given distance. In your example the 7th model in 1MM2 is within 5 Å from
the 7th state of 2kgi, so that gets added to the selection.
> > iterate asdf, print(resi + " " + resn + " " + name + " " +
> str(cmd.distance("tmp", "2kgi///22/CA", "1MM2///" + resi + "/CA")))
>
>
If I understand correctly, here you just get the distances between the
selected atoms, which then gives the output you get.
> 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
>
>
It should work as expected if you split the model into states with
split_states (http://pymolwiki.org/index.php/Split_States) and then make
the selection on just one of those models.
Best regards,
Folmer Fredslund
PS: It's nice to put in you own name
>
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--
Folmer Fredslund
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