Hello Tim It was in one or two versions and I did not get consistent results. However code is there and I can activate it if you want. If you know what criteria you would like to use I can code that also.
In some cases it happens that R/Rfree go up and then they start coming down. It may be case when starting model has not very nice geometry. We are minimising total function. And there are several hidden parameters in the total function (weights between Xray and geometry etc), they may cause problems. Cheers Garib On 25 Aug 2011, at 10:32, Tim Gruene wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hello Ian, > > I dare say that the goal is to get phases which match as good as > possible with what is inside the crystal. If this coincides with > maximising the likelihood, why don't we run refinement until the LL > stabilises? > > @Garib: I have seen runs where Refmac actually does stop "prematurely", > i.e. before the number of cycles set in the input script. It seems that > it stops when LL does not drop between two cycles, but according to Ian > this would be the point to reach. > > My question: does this indeed provide the best interpretable map (be it > cheating or not)? > > Cheers, Tim > > On 08/24/2011 05:36 PM, Ian Tickle wrote: >> Hi Tim >> >> The answer is a definite NO, the goal of refinement is to maximise the >> likelihood from the working set and the restraints. It is definitely not to >> optimise Rfree or LLfree. The correct value of the latter is whatever you >> get at convergence of refinement, i.e. at maximum of the likelihood, >> anything else is 'cheating'. >> >> Cheers >> >> -- Ian >> >> On Wed, Aug 24, 2011 at 4:24 PM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> >> wrote: >> >> 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/ > > iD8DBQFOVgiBUxlJ7aRr7hoRAq+dAKDj2B6iUMD7C4uu8UMznTlKoclYzACdF8nP > Q6DmIFGPcfoP6xbJRwooWWI= > =7r5T > -----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
