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