Hi Charles, When I run the script with all but the first JCH restraints commented out, the script computes the average with the following warning message:
WARNING. No restraints added. However, when I run the script with all but the second JCHB restraints commented out, StructureLoop is called but the average structure is not output. The same warning is also generated. Best regards, Eugene Eugene DeRose, Ph.D. NIEHS NMR Laboratory Manager Global Health Sector SRA International, Inc. Contractor to NIEHS/DIR National Institute of Environmental Health Sciences Research Triangle Park, NC 27709 919.541.1981 voice 919.541.5707 fax derose at niehs.nih.gov www.niehs.nih.gov www.sra.com Enhancing Human Health Around the World Everyday -- On 6/24/10 2:34 PM, "Charles at Schwieters.org" <Charles at Schwieters.org> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello Eugene-- >>> I am trying to use the ensemble.py script to compute a DNA structure using >>> only NOE and dihedral restraints. I have set ensembleSize=3D1 and commented >>> out the dipolar and csa restraints. The calculation runs fine, but does not >>> do the final averaging step. Can anyone suggest what might be causing this >>> problem? >> >> You mean structure averaging in StructureLoop- right? Are there any >> warning or error messages? Which arguments are you passing to >> StructureLoop? >> > I simply tested the script using the sample emsemble.py calculation by > commenting out all the references to the dipolar restraints files and the > following proton setup for loops. In addition, I commented out all the > x-ray stuff. I did not modify the call to the StructureLoop at all. The > only warning message was > > WARNING: this script overwrites the store7, store8, and store9 arrays > > The calculation generated the specified numberOfStructures pdb files, and > tried to run the StructureLoop, but did not output the average structure. > > It appears I can work around the problem by simply commenting out the > potList.append(rdc) line. > So having an (almost?) empty rdc term caused the problem? I'm curious what went wrong, and am also curious why there was no error message in the log. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/><http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkwjpVAACgkQPK2zrJwS/lZWFQCfYDIlXPFzIUmRu9LKnt3tNaGH 22YAn0IwHOzfwHOe/i9Qfth2D+1krqN2 =QEsr -----END PGP SIGNATURE-----
