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Hello Eugene-- >> >>> I am trying to use the ensemble.py script to compute a DNA structure us= >> ing >> >>> only NOE and dihedral restraints. I have set ensembleSize=3D3D1 and co= >> mmented >> >>> out the dipolar and csa restraints. The calculation runs fine, but doe= >> s 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. > > 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. > Are these lines commented out? potList.append(rdcPots) rampedParams.append( MultRamp(0.01,1,"rdcPots.setScale( VALUE )") ) they should be, if there are no RDCs. Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkwk7GgACgkQPK2zrJwS/lZr4wCfQ5IeniXjBRriYaKbM2ApEFQ0 mqMAnRQjyIoB/VLd1OXGagPSiQvrbcxC =SgJx -----END PGP SIGNATURE-----
