Hello Hannah,
I'm glad to investigate if you send me the model file (off-list). It would
also help if you could specify the Phenix version you are using. The only
thing that is coming to my mind without looking at the file is that our
procedure for secondary structure assignment is not finding any SS elements
in your model.
Best regards,
Oleg Sobolev.
On Fri, Oct 15, 2021 at 5:54 AM Hannah Bridges
Hello,
I have a PDB for which, when I run either realspace refinement or validation, phenix does not show rama-z scores for helix or sheet (and the structure is not entirely loops..)
Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.08), residues: 8101 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.06), residues: 8101
It seems peculiar to this one model, as other very similar ones are fine, but is this something that other people have seen before? I can supply the PBD off-list for investigation.
Best wishes
Hannah
-- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom
Telephone : 01223 252812
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