[phenixbb] staraniso/phenix.refine

Gerard Bricogne gb10 at globalphasing.com
Thu Dec 22 09:00:34 PST 2022

Dear Pavel,

     Thank you for your most courteous and constructive reply to my message
that, I must admit, had a few sharp edges. I guess I over-reacted when I
came across the expression "available these days" in your mention of "magic
sticks", thinking that you were referring to a recent newcomer among this
category of programs - i.e. to STARANISO - while absolving the exact similar
sins of the UCLA server ... ;-) .

     This misunderstanding and associated sensitivities now being behind us,
I am in complete agreement with what you wrote to clarify and argue your own
position. It is undoubtedly true that many PDB entries contain too little
experimental data, and that a more proactive involvement of the PDB itself
in formulating guidelines and requirements would have been helpful. Users
have been left for too long without a clear picture of the fact that they
should deposit at least two kinds of corroborating data along with their
models, namely (1) the map coefficients used to compute the map(s) whose
interpretation led to the model being deposited, as this is the most direct
experiment-linked evidence for that model, and (2) the primary diffraction
data themselves that led, along with the model (or even independently from
it, in the case of experimental phasing), to those map coefficients.

     As there can be diverse notions of what is "primary" in this context -
given that the most obvious meaning (i.e. the raw diffraction images) has
remained out of the realm of possibilites for PDB archiving - there has been
a lack of clear guidance or enforcement as to what actual experimental data
should be deposited. As the STARANISO-treated diffraction data have in many
cases provided maps that played a significant role in pinning down certain
key components of final models, it may well have often seemed like killing
two birds with one stone to deposit these data alone as the corroborating
experimental information, introducing a break in the link with raw data if
a description of the nature of that treatment is not included.

     Our reaction to this situation has been to contribute to the creation
of a Subgroup on Data Collection and Processing of the PDBx/mmCIF Working
Group of the wwPDB (quite a mouthful ... ) and to its activities, first
towards extending the mmCIF dictionary to make clearly delineated room for
jointly depositing data before and after treatment with STARANISO (or any
other programs with a similar purpose) together with a description of that
treatment, resulting on March 31st 2021 in the following announcement:

   https://www.wwpdb.org/news/news?year=2021#60638da1931d5660393084c3 .

This extension also tidied up some loose ends towards better supporting the
deposition of unmerged data, with the meaning of that expression at the
time. Since then, a second wave of activity of the Subgroup has been aiming
at further extending the mmCIF dictionary so as to accommodate unmerged data
from serial diffraction experiments, as well as a more richly annotated form
of unmerged data from rotation experiments.

     Given the strength of the concerns you express for the proper archiving
in the PDB of diffraction data as close as possible to the raw measurements,
I hope that you will be lending your support to this initiative, verbally
first but also by contributing to the implementation work on the Phenix side
that is required to make all this fly. You might even consider joining that
Subgroup, so that you can be in the inner loop of the discussions and of the
coordination of efforts. 

     See you in Zoom meetings in the New Year, then ?

     With best wishes,


On Wed, Dec 21, 2022 at 02:53:43PM -0800, Pavel Afonine wrote:
> Dear Gerard,
> I didn't mean to sound unhelpful and if I did I apologize for that!
> What I really meant is this.. I see the growing trend of using
> various data alternation techniques and then not depositing the
> original data but the data changed by these techniques. Clearly if
> this trend exists these techniques must be helpful! However, my
> concern is that by not depositing the original data we methods and
> software developers loose access to these precious original data
> that we could use to further improve the methods. I witnessed
> multiple instances of this happening with UCLA Anisotropy Server,
> for example, or even before that X-plor program allowing some venue
> to sharpen Fobs and then making it easy to continue using the
> sharpened version (that got me at some point!). Or even before that
> the standard practice of cutting off the low-resolution end of data
> set at about 6...8A and worse -- in the absence of appropriate bulk
> solvent models that was actually a good thing to do at that time! Or
> truncating the data by "sigma" (those classic 2-3 sigma cutoffs!) --
> that was also a good thing to do when refinement programs could only
> use LS target functions. And now look in the PDB and see how many
> data sets lack those low-res or weak reflections! So, no, I am not
> picking on a particular tool or method, but I'm picking on the trend
> that makes it potentially easy to permanently loose the original
> data, one way or another, even with a good intention in mind.
> So my real message was and is: any one is of course free to use any
> tools available, but please deposit the original data (along with
> any data used to obtain the final atomic model). Perhaps someone
> uses these data and comes up with even better tools in the future?
> All the best!
> Pavel
> On 12/21/22 08:46, Gerard Bricogne wrote:
> >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,
> >
> >           Gerard.
> >
> >--
> >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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