[PyMOL] Super Bug Report

[David H. <li...@co...>]

In preparing my test for the odd request that I just sent, I came
across what seems to be a bug in super.  It has to do with this weird
nucleic acid thing I was talking about.

Here's the script this time:
from pymol import cmd

cmd.fetch('1acb', async=0)
cmd.fetch('1acb', '1acb_2', async=0)
cmd.fetch('426d', async=0)


print "1acb_2"; print cmd.super('1acb', '1acb_2')[0]
print "426d"; print cmd.super('1acb', '426d')[0]
print "1acb_2_again"; print cmd.super('1acb', '1acb_2')[0]

~> ~/src/pymol_trunk_20100922/pymol -qrkc script2.py
PyMOL>run script2.py,main
1acb_2
0.0
426d
0.0
1acb_2_again
2.80655193329

super should give an rms between 1acb and 1acb_2 of 0.0, which it does
at first.  But once you super your protein to a nucleic acid that has
a calcium ion, when you run exactly the same command, you all of a
sudden get 2.8.  Very weird...

Note, this does not happen if you use 100d, which is a nucleic acid
without a calcium ion, does not happen if you use a pdb file with a
calcium ion, and does happen with 1d56, which is another nucleic acid
with a calcium ion I just pulled out.

In pymol 1.2, it also behaved incorrectly:
~> pymol -qrkc script2.py
PyMOL>run script2.py,main
1acb_2
0.0
426d
nan
1acb_2_again
nan


-David