[phenixbb] staraniso/phenix.refine

Pavel Afonine pafonine at lbl.gov
Sat Dec 17 14:06:26 PST 2022


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.


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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

More information about the phenixbb mailing list