Dear Katherine,
Thanks for pointing this out! As far as I can tell the community has not
reached a consensus on dealing with disordered side chains. I’m afraid it
simply didn’t occur to us, when we were writing the validation task force
report, that one approach would be favoured over the other, and we certainly
didn’t intend to influence community practice by stealth!
This unintended consequence really should have occurred to us, since Gerard
Kleywegt and I had noticed earlier that structural genomics structures
(particularly those from the SGC) have a systematically lower completeness than
other structures, apparently because the choice was made more often to
completely omit poorly-ordered residues rather than include them in the model.
This leaves out many of the residues that would have poor Ramachandran and
rotamer scores, thus raising those scores above the average in a similar way.
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631636/)
Some indication of completeness probably would be a good thing to include in
the validation reports.
Best wishes,
Randy Read
On 10 Jul 2014, at 20:26, Katherine Sippel katherine.sip...@gmail.com wrote:
Hi all,
I've been playing with the new PDB validation service. It is very pretty and
kudos to all the hard work that has clearly gone into it. I did notice
however that the way the information is presented, there seems to be a bias
towards truncating side chains versus modeling them with higher b-factors.
The disordered side chains have higher RSRZs (rightfully so), but there
doesn't seem to be any indicator for missing atoms. As a results I can make
my validation report prettier by truncating versus modeling with high Bs.
I don't want to kick an ant pile here, but given this rather significant
difference in quality reporting, I was wondering if the community had reached
a consensus on this issue that I had missed.
Cheers,
Katherine
--
Nil illegitimo carborundum - Didactylos
--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
