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
Julie
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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