[phenixbb] staraniso/phenix.refine

Luca Jovine luca.jovine at ki.se
Sat Dec 17 00:18:05 PST 2022

Dear Andrea and Julie,

We also encountered the same problem recently, and Clemens and Gerard from Global Phasing (cc:ed) were extremely helpful by quickly adding to the latest (Nov 21 2022) snapshot of BUSTER (https://www.globalphasing.com/buster/) a version of aB_deposition_combine that can correctly merge an autoPROC/STARANISO reflection file with the results of either PHENIX or REFMAC refinement. I personally haven’t tried the latter, but the combination autoPROC/STARANISO + PHENIX mmCIF definitely works (and PDB validation/submission did not complain!).

Have a look here:


Clemens and Gerard, perhaps a note about this could also be added to the autoPROC/STARANISO documentation (if it’s not already there)? Although aB_deposition_combine “belongs” to BUSTER, users may not go search for it there - as opposed to the STARANISO documentation - if they decided to go the PHENIX way…




Luca Jovine, Ph.D.
Professor of Structural Biology, Member of EMBO and the Nobel Assembly
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jovine at ki.se
W3: http://jovinelab.org

From: <phenixbb-bounces at phenix-online.org> on behalf of julie <julie.bouckaert at univ-lille.fr>
Date: Saturday, 17 December 2022 at 08:44
To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] staraniso/phenix.refine

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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,



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