Dear Bernhard,
I will certainly support this, especially frustrating when after all the time spend trying
to describe your density best with solvent/ligands and side/chains
with sum(occ) =< 1 the pdb reports that your structure
is satisfactory/good but the clash score.
Best regards,
Misha
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Bernhard Rupp (Hofkristallrat a.D.) [[log in to unmask]]
Sent: Monday, February 1, 2016 9:47 AM
To: [log in to unmask]
Subject: [ccp4bb] clash crash
Dear Developers/PDBe,
I just finished an otherwise unremarkable structure to the point of my personal level
of tedium, which includes a few correlated partial group occupancies*).
(a) Upon clash checking via coot/probe, the only 5 significant red porcupines involve those
partial occupancies, say a side chain at 0.56 and a close water at 0.44,
the idea that the water is only there when the side chain is in its alternate position.
(b) running the coordinates through
http://wwpdb-validation.wwpdb.org/validservice/
lists exactly and only these 5 as worst ahem ‘errors’ **)
I think it should be reasonably easy to fix the program so that clashes between atoms
with sum(occ) =< 1 are not reported as errors. This *IS* relevant, because remembering the
‘lively discussion’ there was the opinion that the PDB reports should suffice for a reviewer to
judge the quality of a structure model***). As these ‘errors’ also show up in the PDB report, I
see no reason why a reviewer should not simply tell me to clean up that mess (which one really
should – these spikey porcupines usually DO mean something is wrong & fixable).
(c) looking at the next non-severe pinkish clashes, I notice that most involve methyl groups,
and if I eyeball them they are precisely staggered @60 deg around the H3C-X torsion. But when 2 Leu
for example are involved, I doubt that they face off at precisely that torsion angle, because
energetically this is a periodic potential. I think each methyl group torsion would give a little
bit, and voila, pink gone.
In this case, I worry less about the pink, but how is this treated when riding Hs are added in
refinement, for the purpose of improved VdW restraints? Is this torsion potential used (as
in MD) or to we assume the ‘hard’ 60 deg stagger or nothing conformation? Because if the
torsion gives, also the C position might change slightly, ultimately resulting in a more realistic
model. Has anyone played with that?
Thx, BR
*) which is best done at the very very end, because if you renumber residues or sort waters,
the extra occupancy keyword file needs to be changed as well; a process whose tediousness
is better not described. Indicative of errors in this file is a refmac infanticide message
child killed: SIGABRT
**) or is there a more current version of the validation server already online?
***) Ceterum censeo coordinatae densitaeque providati eunt.
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