[phenixbb] staraniso/phenix.refine

Andrea Piserchio andrea.piserchio at gmail.com
Fri Dec 16 17:32:11 PST 2022

 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

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,

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20221216/45746362/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot from 2022-12-16 16-37-18.png
Type: image/png
Size: 53696 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20221216/45746362/attachment-0001.png>

More information about the phenixbb mailing list