So,
Both the phenix-generated mtz file (silly me for not checking this first)
and the cif file generated by aB_deposition_combine can be uploaded on the
PDB server.
Thank you all for your help!!
Andrea
On Sat, Dec 17, 2022 at 5:06 PM Pavel Afonine
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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