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Hi-- > > I am a newer of xplor-nih,i have two questions to seek advice from you . > <1> : I want to generat a PSF file and an extended_structure.pdb > file from one protein seqence. But, > how to generat those two files which Residue_Number started both > from 34 but not started from 1. you can work from the eginput/PSF_generation/genExtendedDNA.py script. Modify the script by chanfing the call to psfGen. Remove the seqType argument, and add the argument startResid=34. > <2> : When i use the same NOE, nbond and dihedral angle constraints > to calculate/refine a protein structure ( started from a extended > initial structure ) seperated in Xplor_NIH 2.13 (I used a modificated > script from protG in eginput ) and CNS . what confused me was that > xplor_NIH gives a higher overall energy and a slower calculation > process on the same computer . > It is a different protocol in the two cases. For analysis of convergence one must look at the rsmd agreement between experiment and calculated structures rather that total energy, because different force constants are used. That said, I think the scripts in eginputs/gb1_rdc are a bit better- you can simply comment-out or remove line 86-109 of anneal.py if you don't have rdcs. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFEAfiZPK2zrJwS/lYRAqUnAJ9yoY6XQ9IbRjX0aTeXB61v4wXrFgCeOjdq QzUx0q8x1XbdtuncDysJU5o= =FyDT -----END PGP SIGNATURE-----
