Yun He wrote: > When I use automodel class to generate N models, the energy MolPDF of every > model will be displayed in the log file, e.g. > =========================================== >>> Summary of successfully produced models: > Filename molpdf > ---------------------------------------- > T0291.B99990001.pdb 2029.54651 > T0291.B99990002.pdb 2719.03467 > T0291.B99990003.pdb 2009.53479 > T0291.B99990004.pdb 2688.20435 > T0291.B99990005.pdb 2311.00342 > =========================================== > But, sometimes, after the models got be refined by some other means, how can I > get those changed molpdf by handling the existed PDB files, rather than to > involve the automodel class again to rebuild such models?

The PDB files produced by Modeller also contain the molpdf, as a REMARK at the top of the file, so you can just read this. If you refine the structure, you should write out a new PDB file, which will contain the refined structure and molpdf.

> I think "examples/commands/energy.py" in node151.html of the manual may help > me, but I wonder whether the molpdf got by this method is identical to that > recorded in log file.

The molpdf will only be the same if you use the same set of static restraints (.rsr file) and dynamic restraints (i.e. combination of soft sphere with statistical potentials, and cutoff distances).

Ben Webb, Modeller Caretaker