And I usually accept the TLS domain definition, but reset all B factors and start B factor refinement again - ie dont use the actual TLS numbers returned.. Ideally I guess the B reset could be done using TLSANL
There seems to be confusion over the interaction between the iso B and those TLS generated ones.. Eleanor On 18 June 2015 at 22:08, Boaz Shaanan <bshaa...@bgu.ac.il> wrote: > Hi Christian, > > I usually send the pdb back to the tlsmd server after any manipulation of > the model just to be on the safe side. I'm not sure whether that'll make > any difference in your case but it's perhaps worth trying. > > Cheers, > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Christian > Roth [christian.r...@bbz.uni-leipzig.de] > Sent: Thursday, June 18, 2015 11:30 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Refmac refinement R factors going up..... TLS issue? > > Hi all, > > I refine a structure with TLS and restrained refinement in Refmac. After > the run finished, I fixed a few outliers manually in Coot, saved that > file and used that with the original TLS file from TLSMD for the next > round of refinement. As soon as the restrained refinement starts the > R-factors are going up and stabilise than at a higher values compared to > the previous run. > If I switch of the TLS refinement and just do restrained refinement with > the same input files the R-values start initially at a higher values and > than decrease till they stabilise. Unfortunately the final values are > about 1.5 % higher, compared to the run with TLS before manual > rebuilding. So TLS seems to me beneficial and I would like to use it, > but somehow a strange combination of wrong files?, wrong > parametrization? or whatever prevent me of doing that. > Has anyone an idea what might be the cause of that strange behaviour. > > Thank you very much in advance. > > Cheers > > Christian >
