[phenixbb] staraniso/phenix.refine

Pavel Afonine pafonine at lbl.gov
Wed Dec 21 14:53:43 PST 2022

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!

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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