Example of molecular dynamics/simulated anneanling structure determination using distance, torsion angle, and bond-vector orientation (from RDCs) restraints, as described in detail in: C.D. Schwieters, G.A. Bermejo, ``Protein Structure Elucidation from NMR Data with the Program Xplor-NIH,'' Methods Mol Biol. 1688, 311-340 (2018). [available here as chapter.pdf] --------------------------------------------------------------------------------------- Run the following programs (in the order in which they appear): # Generate a PSF file from sequence. seq2psf gb1.seq # Calculate a set of structures starting from extended conformations. xplor -py fold.py > fold.log # Return a symbolic link to the top-scoring structure calculated by fold.py. getBest -num 1 -symlinks # Calculate a set of structures by refining the top-scoring one from fold.py. xplor -py refine.py > refine.log [ Running these commands requires that the Xplor-NIH helper programs are in your PATH. This can be accomplished by adding the bin directory of the Xplor-NIH distribution to your PATH, or using the -symlinks option to ./configure so that the commands are available from a directory already in your PATH. ] --------------------------------------------------------------------------------------- fold.py is exactly as presented in the reference, except for the following changes: * The nstructures variable has been added at the very beginning to specify the wanted number of structures.