Hi Thomas and David,
Thanks for bringing this to my attention. PyMOL was indeed trying to
fit to a degenerate case. I fixed the bug: PyMOL will now print:
ExecutiveAlign: No alignment found.
and leave your objects untouched.
This fix is mixed in with some other development code, so I'll extr
Hi David,
this is bug, indeed. I also hit this some time ago but didn't report it
so far. The actual problem is that the cmd.super('1acb', '426d') fails
completely and only aligns a single atom, resulting in a Null-matrix
that collapses all of 1acb into a single point. The RMSD of 2.8 that you
get
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.fe
