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

[Marcin Wojdyr]

Hello Carlos,

Thanks for reporting this problem. I don't know what went wrong here.
It'd be good to track it down, but I'm not able to reproduce it.

How did you discuss it with the PDB people? If by email, could you
forward it to me?

Thanks,
Marcin

On Tue, Dec 3, 2024 at 4:27 PM Kikuti Carlos via buster-discuss
<buster-discuss at globalphasing.com> wrote:
>
> 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:
>
> To warn you about this;
> 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
>
>
>
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