I sent this question to the solve/resolve listserver but didn't get a response, so I'm sending it to the ccp4 listserver.
My question is about getting different results from different versions of solve/resolve. I compared Se-Met SAD calculations using these three versions of solve/resolve: 1. solve version 2.11 of 12-May-2006/resolve version 2.11 of 31-May-2006 2. solve version 2.13 of 26-Jan-2007/resolve version 2.13 of 01-Feb-2007 3. solve version 2.13 of 2-Jul-2007/resolve version 2.13 of 23-Jun-2007 Each calculation used the simple script listed below and a Se-Met SAD data set that we used a few years ago to determine a structure with solve/resolve version 2.06. In calculations 1 and 2, solve found 13 sites and resolve traced almost the entire chain, which is the expected result. For case 3, however, solve found 12 sites, the resolve map looks bad and the trace is nonsense. My question is whether anyone else has encountered similar issues with these particular versions of solve and resolve 2.13. I note that in case 3, resolve is dated earlier than solve. Could that be a problem? Thanks very much. Jack Tanner -------------------------------------------------------- #!/bin/csh mkdir sad1 cd sad1 # # solve.com file to run SOLVE/RESOLVE version 2.01 # # set CCP4 and SOLVETMPDIR and SYMOP variables: # setenv CCP4_OPEN UNKNOWN setenv SOLVETMPDIR /var/tmp setenv SYMINFO /linux/lib/solve/syminfo.lib setenv SYMOP /linux/lib/solve/symop.lib # # use all system resources: # unlimit # # # command file to solve an SAD dataset (Pt 1-wavelength) # # solve_huge<<EOD > solve.log logfile solve.logfile resolution 20 2.0 cell 72.0110 91.4545 69.5427 90.0000 119.1841 90.0000 symfile /linux/lib/solve/c2.sym readtrek ! readformatted/readdenzo/readtrek/readccp4_unmerged premerged ! premerged/ unmerged read_intensities ! read_intensities/read_amplitudes fixscattfactors ! fixscattfactors/refscattfactors mad_atom Se ! solve recognizes selenium atom type lambda 1 label SAD data for Se-Met rawmadfile ../datafiles/dtscale_merge_peak.ref fprprv_mad 7.2 ! f double prime at this lambda nsolsite_deriv 18 ! search for this many sites max nres 312 !number of residues in asu nanomalous 18 !number of anomalously scattering atoms in asu SAD ! solve an SAD dataset EOD # # Now do density modification and build a model: resolve_huge<<EOD>resolve.log solvent_content 0.58 seq_file ../datafiles/puta52.seq ! sequence file EOD # All done; your output phases are in resolve.mtz and # your model is in resolve.pdb # -------------------------------------------------------- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building 601 S. College Ave. Columbia, MO 65211 573-884-1280 (office) 573-884-1280 (lab) 573-882-2754 (fax) http://www.chem.missouri.edu/TannerGroup/tanner.html -- ------ End of Forwarded Message
