I realize this is an edge case, where behavior is not always well
defined in programs, but I have a request for a behavior (and the
behavior actually seemed to change between 1.2 and 1.3)
My example script:
from pymol import cmd
cmd.fetch('1acb', async=0)
cmd.fetch('1acb', '1acb_2', async=0)
cmd.fetch('100d', async=0)
cmd.fetch('426d', async=0)
print "1acb_2"; print cmd.super('1acb', '1acb_2')[0]
print "1zna"; print cmd.super('1acb', '100d')[0]
print "426d"; print cmd.super('1acb', '426d')[0]
To explain, 1acb is a protein, 100d is a nucleic acid, 426d is also a
nucleic acid, but with a calcium, whose CA atom seems to impact the
behavior of super. I want to be able to tell that 1acb and 1acb_2 are
identical.
In 1.2, when I ran this:
> pymol -qrkc script.py
PyMOL>run script.py,main
1acb_2
0.0
1zna
ExecutiveAlign: invalid selections for alignment.
2.79037312189e-38
426d
nan
I can see that 1acb_2 is different from the others. I like the 426d
behavior or reporting "nan", but I can deal with looking for the
ExecutiveAlign error I see with 100d.
In pymol trunk, when I ran this:
~> ~/src/pymol_trunk_20100922/pymol -qrkc script.py
PyMOL>run script.py,main
1acb
0.0
1zna
ExecutiveAlign: invalid selections for alignment.
0.0
426d
0.0
I can still look for the ExecutiveAlign error for 100d, but I don't
have any indication of differences between 426d and 1acb. In this
case, I can do rms_cur or something to differentiate them, but in my
real desired use case, this is not possible.
I would love it if in the case of errors in alignment or rms, when
there are no atoms used or matching, it would return nan as it used to
for 426d. If you think I should just stop doing silly things like
trying to use pymol's super to tell if a pdb is a nucleic acid, that's
an understandable response though.
-David
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