[phenixbb] missing statistics for rama-z

Oleg Sobolev osobolev at lbl.gov
Fri Oct 15 09:16:44 PDT 2021


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 <hrb at mrc-mbu.cam.ac.uk>
wrote:

> 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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20211015/e04dd3e2/attachment.htm>


More information about the phenixbb mailing list