Hi Pavel,

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

Short explanation is presented in the output itself:

Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.

Slightly longer explanation can be found in the paper (https://doi.org/10.1016/j.str.2020.08.005), STAR Methods section:

It should be noted, that Secondary structure-dependent Rama-Z scores and the Rama-Z score for the whole model are related in an unobvious way: the scores for helices, sheets, loops and the whole model were calibrated separately to achieve a mean score of 0 and an RMSD of 1 for the reference models, therefore the calibration values are different. This becomes obvious in some corner cases: for example, if the whole model does not have any helices and beta-sheets, the score for loops and for the whole model will be different.

Best regards,

Oleg Sobolev.

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@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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