[buster-discuss] PDB Validate doesn't like mmCif file from Buster

[Kikuti Carlos]

Hello,

I haven’t seen this discussed anywhere yet. Our PhD student has been struggling to get her models judged by the PDB Validate server, as we usually do before submission to the PDB.

The problem seems to come when Validate tries to calculate the map and CCs. Upon discussion with the PDB crew, the instruction she had was to REMOVE lines 16-27 from the mmcif file. Then it worked. The contents of the unwanted lines are the following:

loop_
_entity.id
_entity.type
A polymer
MG! non-polymer
ADP! non-polymer
VO4! non-polymer
ZZZ! non-polymer
EDO! non-polymer
SO4! non-polymer
CL! non-polymer
water water

(I can’t publicly share the entire mmcif file at this point. “ZZZ” is a ligand )

Previous structures from her contained those lines and where accepted, so we believe there was a recent update in Validate that started to bother with them.

So for the next rounds of Validate, we’ll remove those lines before uploading – which is all right, but I just wanted:

  1.  To warn you about this;
  2.  To ask if you have other suggestions of routines, other than uploading to Validate for this kind of pre-submission test? We use the validation tools in Coot and Molprobity, but for some reason the criteria and the calculated maps are not exactly the same as for the PDB… It would be much easier to have this validation running locally, just to avoid the uploading interface.

 Looking forward to your replies,

---------------------------------------------------
Carlos KIKUTI, PhD
UMR144 - CNRS - Institut Curie
Pavillon Trouillet Rossignol
26 Rue d’Ulm - 75005 Paris, France
+33 6 82 87 62 76
carlos.kikuti at curie.fr<mailto:carlos.kikuti at curie.fr>

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