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salilab / IHMValidation

Validation software for integrative models deposited to PDB
MIT License
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Misleading message about the number of bond outliers #59

Open aozalevsky opened 1 year ago

aozalevsky commented 1 year ago

Even if no outliers were detected (which means that everything is ok), the following message is printed:

Standard geometry: bond outliers[?]
Bond length outliers can not be evaluated for this model

Also incorrect formatting for the number of angle outliers:

Standard geometry: angle outliers[?]
There are 628 angle outliers in this entry (62800.0% of all angles). A summary is provided below, and a detailed list of outliers can be found

To be fixed here https://github.com/salilab/IHMValidation/blob/c3bb0ef65f6104368a103ee429dcf264285ba936/templates/model_quality.html#L60

Entries for testing: 9, 55, 141

After the fix all reports have to be updated.

aozalevsky commented 3 months ago

Sometimes it's not possible to reliably detect the total number of bonds from the molprobity output. I'm trying to figure out what triggers the difference in the output. In the meantime, this is a temporary workaround that doesn't calculate the percentage if we don't get the total number of angles.