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Re: [modeller_usage] How can I get MolPDF of an existed PDB file of an model



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
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