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
>> [...]
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