Hello,

In the end of the log-file from a MODELLER (8v1) run there is a summation of the quality of the model:

>> Summary of successfully produced models: Filename molpdf ---------------------------------------- A.B99990001.pdb 2355.08740 N.B99990002.pdb 2376.38696 ... ...

My question now is if these values really are the molecular pdfs or if it is the objective function?

The reason I am asking is, that we have built homology models of the same protein two times using the same sequence alignment and template pdb-files only changing the refinement level - one is the default the other is md_level = refine.slow_large.

In the second run the values in the log-file range around 9000. If the value really represents the mol PDF this is good, but if it is the objective function, the first models (default refinement) with the lower values are much better...

Another question: What is the default level of refinement actually? I have not been able to deduce this from the manual.

I hope someone can help me with this:-)

Thanks in advance Leyla