Hi Charles, This works with all but the JCHB restraints commented out, but I still get the warning message, so there still seems to be problem if only one set of restraints is included. However, the average structure is still not output, when I comment out all the dipolar restraints and the potList.append and rampedParams.append statements. For now, I guess I should be able to exclude the contributions from the dipolar restraints by just commenting out these two statements.
Thanks again, Eugene On 6/25/10 1:50 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 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/><http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkwk7GgACgkQPK2zrJwS/lZr4wCfQ5IeniXjBRriYaKbM2ApEFQ0 mqMAnRQjyIoB/VLd1OXGagPSiQvrbcxC =SgJx -----END PGP SIGNATURE-----
