[phenixbb] missing statistics for rama-z

[Oleg Sobolev]

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 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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>
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