[phenixbb] staraniso/phenix.refine

julie julie.bouckaert at univ-lille.fr
Fri Dec 16 23:40:01 PST 2022

Dear Andrea

I also experienced that the PDB cannot appreciate the 
Data_1_autoPROC_STARANISO_all.cif file due to the lack of Rfree set. 
This would be solvable, like in Refmac5 (CCP4i2), if you can upload 
second reflection file that contains the free R flags used for refinement?

- However, CCP41/Refmac5 does not (yet) read .cif reflection files. As 
far as I know, Phenix Refine does not (yet) neither.

- But Refmac5 does merge two .mtz reflection files into a sinlle 
hklout.mtz that you can find under job1 directory. This is what I 
currently use to deposit to the PDB.

- I understand .cif files (both model and reflections) have the 
advantage that they are editable. Perhaps there is a good reflection.cif 
file editor around?

- A solution would be to have the option during PDB deposition, of 
adding the reflection file used for refinement and thus containing the R 
free set, that are then automatically recognized as reflection files and 
merged (like for hklout.mtz in Refmac where this option was probably 
incorporated for re-refinement with re-processed data).

Problem today is that only one reflection file is permitted and you 
would indeed not get the correct validation report outputted.

In other words, one data file from crystal data, and another one for 
crystal refinement and including map coefficients, or like we do it in 
the lab, would allow compatibility with different ways of re-refinement 
and perhaps the independence from the EDS server (that failed on me last 
week, meaning there are no electron densities in the validation files 
and meanwhile the submission is "locked" and also no answer from the PDB 
staff yet, so what do we do: we submit the poor validation file to the 
journal and be more subject to rejection by reviewers. What I prefer, 
seen the current situation, is to send reviewers the model coordinates 
and map coefficients).

all the very best


On 17/12/22 02:32, 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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_______________ Julie Bouckaert , chercheur CNRS UMR 8576 à l’Université 
de Lille 
Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) IRI, Office 
131, 50 Avenue de Halley, 59658 Villeneuve d’Ascq, France Tél. +33 (0) 
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