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
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