[phenixbb] on the criteria for outliers, phenix.molprobity and wwPDB validation

[Jorge Iulek]

Thanks, Pavel, for your remarks.

J.

On 4/26/24 16:48, Pavel Afonine wrote:
> Hi Jorge,
>
> Possible reasons for discrepancies include:
>
> - Different versions of libraries used (Phenix always uses the latest 
> provided by Richardson's lab).
>
> - Different libraries (e.g., Phenix uses CDL natively).
>
> - Explicit presence or absence of H atoms, and how they are treated by 
> the software.
>
> Clearly, we won't be very enthusiastic about using outdated libraries 
> to match others'.
>
> Most of the time, the differences stem from 'borderline' cases where 
> residues contributing to differences are located at or very close to 
> contour lines that separate outliers from allowed, or allowed from 
> favorable.
>
> In the case of CDL, the idea of an 'ideal' value is a sort of moving 
> target as it depends on the local conformation. In such cases, you 
> won't be able to match other software unless they also use CDL.
>
> All in all, with this knowledge at hand, if you manage to convince 
> yourself (and, if required, others) that the observed differences are 
> insignificant, then all is just fine!
>
> Pavel
>
>
> On 4/26/24 11:39, Jorge Iulek wrote:
>> Hi all,
>>
>>
>>     I had already noticed that outliers spotted by phenix with its 
>> validation tool, with the nice feature to carry one straight to the 
>> "suspicious" residue in a coot session for visual inspection, differs 
>> a bit from what comes spotted from wwPDB validation, generally the 
>> latter spotting some few more residues.
>>     To one current structure, which at low resolution, I notice there 
>> is a bit larger difference between the number of spotted residues.
>>     I see from wwPDB validation, molprobity is also used to spot 
>> outliers for many of the analyses. I see the current molprobity 
>> version used is 4.02b-467, but I could not yet devise the molprobity 
>> version used by phenix. Of course, there would also be the "library" 
>> used in each case to spot the outliers. Maybe someone ever listed 
>> what is considered in each case, and their differences, or a link to 
>> that is welcome for me.
>>     What would be the best criteria for spotting is of course a good 
>> discussion. But a superficial question I would make is if there is a 
>> way to make phenix.molprobity output to resemble the one from wwPDB 
>> validation, at least the ones accounted by molprobity?
>>
>> Jorge
>>
>>
>> _______________________________________________
>> 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/20240429/ba94dd88/attachment.htm>