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 extract
it and check it in soon.
Cheers,
-- Jason
On Thu, Sep 23, 2010 at 3:05 AM, Thomas Holder
<spel...@users.sourceforge.net> wrote:
> 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 your last call is just an artefact that arises from aligning the
> correct protein to the collapsed one. Just run your example with GUI and
> you see what happens.
>
> fetch 1acb
> fetch 426d
> copy 1acb_2, 1acb
> super 1acb, 426d
> super 1acb, 1acb_2, object=aln
> zoom aln
>
> I think the super command should check if the resulting matrix is
> orthonormal or at least not a Null-matrix.
>
> Cheers,
> Thomas
>
> On Wed, 2010-09-22 at 18:28 -0400, David Hall wrote:
>> 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
>
> --
> Thomas Holder
> Group of Steffen Schmidt
> Department of Biochemistry
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
>
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