Hi Harry,
(Oooh - after lurking on this list for probably 20 years, I can actually
comment on something...)
If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of
structures that fit the NOEs, is there a tool available that will
give me some idea about the bits of the structure that do not vary
much (“rigid”) and the bits that are all over the place
(“flexible”)?
I used to use a tool called "uwmn", originally written by Mike Hartshorn
when he was in York, and extended a bit by myself.
This calculated a "mean interatomic distance matrix" over all the
structures in an ensemble, for the atoms selected on the command-line
and then projected it back into 3D (using PCA, or possibly PCoA - I
can't remember which) to make an "unweighted mean" structure.
It then looped over all the individual structures to calculate a
least-squares fit to the mean structure, and populated the B-factor
field with each atom's deviation from the "mean" coordinate.
To solve your problem, I would have first run it on the CA's of the
whole chain, and looked at the "B-factors" to see where the variability
was greatest, then iteratively excluded/included bits of backbone until
I thought I had a structurally-legitimate selection for the
not-so-variable regions. Convincing novices to check the ensemble
visually was an important part of this, I recall.
I'd love to recommend you use Mike's/my code, but I'm not sure whether I
can find a copy, nor whether it will compile on a modern Linux. I'll
try to dig it out...
Best regards,
Andrew
--
Dr. Andrew Raine, Head of IT, MRC Mitochondrial Biology Unit,
Keith Peters Building, Biomedical Campus, Cambridge, CB2 0XY, UK
phone: +44 (0)1223 252830 web: www.mrc-mbu.cam.ac.uk
email: [email protected]
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