[phenixbb] staraniso/phenix.refine

Gerard Bricogne gb10 at globalphasing.com
Wed Dec 21 08:46:05 PST 2022

Dear Pavel,

     I thought I ought to respond to the second paragraph of your message,
as I find it rather disappointing that you chose to deal with this matter in
such a dismissive and unhelpful manner.

     When users decide that they are willing to go to the trouble of trying
to deposit the data produced by STARANISO, it is presumably because they
derived some benefit from using it as input into building and/or refining
their model. Clemens has "walked the extra mile" to enable the deposition of
such data along with refinement results obtained not only with BUSTER but
also with REFMAC and phenix.refine, out of a desire to enable users to do
what they want to do, rather than try and dissuade them from it.

     You deride "available these days magic sticks (that "correct" for
anisotropy, sharpen or else!)". The UCLA Diffraction Anisotropy Server has
been doing exactly that for over a decade and a half without incurring this
kind of sarcasm. As for objecting to corrections, sharpening and truncation,
should that extend to the upscaling of higher-resolution data by image-wise
B-factors and to the rejection of outliers, all of which take place in every
single scaling and merging job? Probably not - so this remark sounds more as
if it is just gratuitously picking on STARANISO rather than offering helpful
advice to users.

     With best wishes,


On Sat, Dec 17, 2022 at 02:06:26PM -0800, Pavel Afonine 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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