On Friday, 13 June 2014 10:12:50 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?
See the other thread "ccp4 ligand tools + wwPDB validation = bug reports"
Because the error is not in a pre-packaged cif file.
Nor is it in a ccp4 program per se.
It is in a library that is used by cprodrg to generate a cif file
for previously unknown ligands.
This library originally came from the Dundee folks,
not ccp4, and it was not clear who if anyone was maintaining it.
In an admirably quick response, Alexander Schuettelkopf has now
expressed his willingness to respond to such bug reports and update
the library.
So that's good news for cprodrg, and I gather that indeed the fixes
will appear in future ccp4 updates.
But the problem is more general.
For example, I have had analogous problems with Grade.
There again it is clear that this can affect other ccp4-ers,
so ccp4bb seems to me a good place to mention any bugs or quirks that
contribute to structure refinement errors so that others are aware of
potential problems. The eventual fix may have to come from elsewhere
(e.g. GlobalPhasing in the case of Grade). Unlike prodrg, the Grade
code and libraries so far as I know are not available for inspection or
patching locally.
Paul Emsley has Emailed my separately that there is a new project
ACEDRG in the offing that may take over the prodeg/Grade niche inside ccp4.
Perhaps someone involved in ACEDRG will post a summary of what it
will offer?
cheers,
Ethan
>
> 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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