but it was related to very different use case (template of very low
identity), and the answer omits the relation to molpdf. The modeller
documentation on DOPE score and the 2006 DOPE paper say, that it was
designed to choose the best model. However, this value is not printed
out by default neither appear in the detailed evaluation of local model
problems presented in the tables of restraints violations.
The fact that molpdf only is selected as the default score of model
quality makes DOPE at little suspicious. I mean, it looks like there was
a reason to hide it. In my case, my models are good enough to all have
GA341 scores equal to 1, what makes this value useless. Still, molpdf
and DOPE do not correlate, so which one shall I consider more important
for model choice?
I see from my experience that molpdf is rather sensitive to the choice
of templates (e.g. the same protein template from X-ray vs NMR can give
very different molpdf values of models, with much more restraint
violations for NMR). Also, if one is using multiple templates for the
same sequence, the molpdf values are closer to ones obtained using
single worst template than to using the best one, while DOPE values do
not change much. These observations would count against relying on
molpdf, but if molpdf is misleading, then the entire verbose analysis of
restraint violations from which molpdf is calculated must be equally
misleading.
Could you share your insight and comments?
With regards,
Paweł Kędzierski
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