Dear Tim At the moment there is no option to stop refmac prematurely. I can add if it is necessary. I can only give my experience. After molecular replacement before running ARP/wARP or buccaneer I usually run 60-100 cycles of refinement with jelly body with sigma set to 0.01. Then automatic model building works better. I have seen this behaviour in several cases (if there are more than one copy I also would use local ncs restraints). Using jelly body slows down convergence but shifts seem to make more sense.
regards Garib On 24 Aug 2011, at 17:24, Tim Gruene wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear all, > > especially at the beginning of model building and/or at low resolution > both Rfree and "-LL free" as reported in the refmac logfile show a > minimum at a some cycle before rising again. > > I am certainly not the only one tempted to first run refmac with a large > number of refinement cycles, determine that minimum and rerun refmac > with ncyc set to that minimum. > > Of course I want the resulting model and phases/map to be as close to > the what's in the crystal as possible in order to facilitate model building. > > Is it therefore good practice to interrupt refmac wherever it finds a > minimum (if so, the minimum w.r.t. which number reported in the log-file)? > > Thanks for everyone's opinion and experience, > > Tim > > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.11 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFOVReTUxlJ7aRr7hoRAqyzAKCZpMJPVSQJTDEoWGxZEymwvqfFcACeMNLL > rvIDPlXiL5HQmoNm7yrTt6k= > =UnKT > -----END PGP SIGNATURE----- Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
