Hello everyone.
Many thanks for the thoughts on the matter.
Dear Dr Abhinav
You can try to run a simulated annealing in CNS and then try to refine that
> model and see if that solves the problem. This would most likely help in
> getting rid of the overfitting problems.
>
I have trouble installin
Hello, unless it's changed over the last couple of years, the pdb rightly used
to let you deposit a structure with outliers, hopefully not too many, though ;-0
I take it the stalling you reported probably comes from whoever is looking over
your shoulder.
Best wishes, Jon Cooper. jon.b.coo...@pr
Hi
I think It may be worthwhile submitting your model and data to PDB-REDO to see
if (inter alia) you have applied any unconscious bias to your building that has
resulted in these outliers, or over- or under-interpreted the data. It’s quick
and easy to submit and requires remarkably little effo
A good example of such expected outliers can be found in structures of
nucleosomes: the validation report always flags almost all DNA bases as
geometry outliers. But we have no end of evidence that these structures are
correct: for instance, the many ensemble and single-molecule FRET studies of
Well - some outliers are infix able! There are various reasons - floppy
residues like arg or lys
In multiple positions; strain due to protein folding constraints, etc.
I use the validation report to check for obvious modelling errors but if
you can’t find any, you have to just submit the results o
Dear all
We have refined (Refmac5) a crystallographic structure with Rw/Rf values
0.19/0.22 (Resln 2.67). However, the deposition has stalled on account of
the wwPDB's preliminary validation report, which indicates map/model and
geometry issues, with each criterion containing a few instances. We t
