[phenixbb] staraniso/phenix.refine

[Andrea Piserchio]

So,

Both the phenix-generated mtz file (silly me for not checking this first)
and the cif file generated by aB_deposition_combine can be uploaded on the
PDB server.

Thank you all for your help!!

Andrea

On Sat, Dec 17, 2022 at 5:06 PM Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi,
>
> two hopefully relevant points:
>
> - phenix.refine always produces an MTZ file that contains the copy of
> all inputs plus all is needed to run refinement (free-r flags, for
> example). So if you use that file for deposition you have all you need.
>
> - Unless there are strongly advocated reasons to do otherwise in your
> particular case, you better use in refinement and deposit the original
> data and NOT the one touched by any of available these days magic sticks
> (that "correct" for anisotropy, sharpen or else!).
>
> Other comments:
>
> > - However, CCP41/Refmac5 does not (yet) read .cif reflection files. As
> > far as I know, Phenix Refine does not (yet) neither.
>
> Phenix supports complete input / outputs of mmcif/cif format. For
> example, phenix.refine can read/write model and reflection data in cif
> format. It's been this way for a long time now.
>
> Pavel
>
>
> On 12/16/22 17:32, Andrea Piserchio wrote:
> > Dear all,
> >
> >
> > I am trying to validate and then (hopefully) deposit a structure
> > generated using the autoproc/staraniso staraniso_alldata-unique.mtz
> > file as input for phenix.refine.
> >
> > Autoproc also produces a cif file ( Data_1_autoPROC_STARANISO_all.cif)
> > specifically for deposition.
> >
> > Long story short, the PDB validation server complains about the lack
> > of a freeR set for both files. I realized that, at least for the cif
> > file, the r_free_flag is missing (but why does the .mtz for the
> > isotropic dataset work??),so I then tried to use for validation the
> > *.reflections.cif file that can be generated by phenix.refine. This
> > file can actually produce a validation report, but I still have some
> > questions:
> >
> > 1) Is it proper to use the .reflections.cif file for this purpose?
> > During the upload I do see some errors (see pics); also, the final
> > results show various RSRZ outliers in regions of the structure that
> > look reasonably good by looking at the maps on coot, which seems odd ...
> >
> > 2) In case the *.reflections.cif is not adequate/sufficient for
> > deposition (I sent an inquiry to the PDB, but they did not respond
> > yet), can I just add a _refln.status column to the autoproc cif file
> > (within the loop containing the r_free_flag) where I insert “f” for
> > r_free_flag = 0 and “o” everywhere else?
> >
> >
> > Thank you in advance,
> >
> >
> > Andrea
> >
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>
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