Do those fixes also make it to the phenix version of the library? Yes,
this is the CCP4bb, but the monomer library is also used by Phenix, and
a good number of structures (almost half of those deposited this year?)
in the PDB now come from phenix.refine. Or in other words, is there a
central, high quality monomer library shared among the two most common
refinement programs? (The phenix version is more like a fork of the
CCP4, I think.)
And not all fixes are obvious. Think of the thread from June 4 this year
about XYP and HSZ.
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;e617308e.1406
The atoms here have non-standard numbering, which would break the way
sugar linkages are defined (and sugar linkages in glycoproteins are just
as standard as peptide linkages are in glyco- and non-glyco-proteins.)
Would this be fixed, or not, I am not sure.
I think it might encourage those of us who spot these errors to report,
if there was a clear call for, or a place to submit these errors. CCP4bb
might be that place; that should depend on what Garib and the phenix
folk prefer.
Engin
P.S. I should, as always, say that while the libraries we use are
imperfect, without them the situation would be much, much worse, so many
thanks to Garib et al for their hard work.
On 6/13/14, 3:12 AM, Tim Gruene wrote:
Hi Ethan,
Maybe I miss something, but whenever an error in one of the cif-files
has been reported, be it directly to Garib, or publicly on the ccp4bb,
Garib (I assume) fixed very quickly - I don't quite understand why we
need a new term for this process?
Best,
Tim
On 06/12/2014 10:45 PM, Ethan A Merritt wrote:
[...]
Indeed. All of the library-generation tools I am aware of are flawed in
their own idiosyncratic ways. I think I shall start a campaign to treat
errors in the cif libraries as "bugs", and encourage people to report
these bugs in the libraries we all use just as they do for bugs in the
programs we all use.
Ethan
[...]
