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

[Clemens Vonrhein]

Dear all,

On Wed, Dec 04, 2024 at 12:20:17PM +0000, Kikuti Carlos via buster-discuss wrote:
> Hello !
> 
> Marcin, I’ve just sent it to your e-mail, thank you.

If you could share that email with us as well, we would be very
interested in the detail warnings/errors reported. After all, the
PDBx/mmCIF files produced by BUSTER (BUSTER_model.cif and
BUSTER_refln.cif, via the aB_deposition_prep tool) use Gemmi
internally - but with a few small changes/adjustments to get to those
final files. Or if you combine the deposition-ready mmCIF files from
autoPROC+STARANISO with those from BUSTER (using the
aB_deposition_combine tool) there would even be some more
steps/adjustments involved. It might be that we're doing something
wrong in those Gemmi-indpendent parts.

Having said that, I just ran some validation jobs using a
BUSTER_model.cif and BUSTER_refln.cif files as they come out of BUSTER
(see below) without any issues: no warning/error reported in any of
the output/log files.

> If you or anybody else has ideas concerning the second part: “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.”  … I’m all ears.

I tend to use the wwPDB validation via the OneDep API using the
onedep_validate_cli python module: this can easily be scripted so that
I only have to do

  refine/aB_autorefine ... -d outdir ...
  cd outdir
  validate_buster.sh

At least: it works for me on Ubuntu 22.04. Let me know if you are
interested in more details ... however, this still involves uploading
of those BUSTER-produces mmCIF files to the validation server (through
the API instead of the web interface), so might not fit your exact
needs here.

Cheers

Clemens