[phenixbb] missing statistics for rama-z

[Pavel Afonine]

Hi Oleg,

I'm also curious why for the same amount of residues 8101 two numbers 
for 'whole' and 'loop' are different?

Pavel

On 10/15/21 09:16, Oleg Sobolev wrote:
> 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
>
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