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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