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The MAKE_U_POSITIVE problem may be genuine, i.e. some parts of your structure don't fit the assumptions of the TLS model. In which case, sure, leave them out. Or it may simply be a symptom of the refinement protocol. Starting with fixed constant Bs allows the TLS full freedom to describe the displacements. But maybe too much freedom. In which case, having some variation in the Bs is useful. One protocol is to keep the residual Bs from one round, and start the TLS parameters from zero again. Regards Martyn On Wed, 8 Feb 2006, Christian Schleberger wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Dear all! > > I am refining a structure against a 2.1 A resolution remote dataset of a > Se-Met MAD experiment. Since the R/Rfree is stuck at 21/27 % I tried to > use TLS refinement. This yielded a much better R/Rfree of 19/24.1 but I > got this 'Problem in MAKE_U_POSITIVE' warning. Analysing the models > before and after TLS showed the following results: > > no ncs, no tls: > average B (overall) > chain A: 48.7 > chain B: 45.6 > chain C: 33.9 > chain D: 20.2 > > R/Rfree 21/27 % (CNS gives nearly the same results) > > > no ncs, one tls group per protomer: > average B (overall) > chain A: 13.1 > chain B: 12.9 > chain C: 14.5 > chain D: 12.9 > > R/Rfree 19/24.1 > > tlsanl and different refmac trials with fixed starting Bs for subsequent > tls refinement (35-60) showed that protomers C and D seem to cause the > problems. Therefore I tried a refinement protocol with just chains A and > B in two different tls groups, leaving out chains C and D. > > no ncs, tls on protomers A+B: > average B (overall) > chain A: 28.4 > chain B: 28.5 > chain C: 34.6 > chain D: 21.8 > > R/Rfree 20/26 > > The matrix weight was 0.17 in all cases. Bbulk was fixed to 200 (refined > to 295 without fixing) > > I would like to know if it is legitimate to use tls only on parts of the > asymetric unit and/or if there are any other things I should look for. > > > additional informations: > The structure solution was straight forward. The experimental density > for all 4 subunits was good. > > spacegroup: P2(1) > cell axis: 90.570 57.020 152.697 90.000 103.352 90.000 > > wilson B from XSCALE: 33.23 > > Rsym (overall/last shell): 5 (25) > reflections: 86204 (7972) > > overloads: 143 out of 1343616 > > As far as I can see the data looks good so far. the Wilson line is ok > according to what I see in truncate. > (it didn't pass the arp/warp check, but until now I haven't come across > a dataset that passed it). > The dataset doesn't show any sign of radiation damage (checked this > looking at the xdsstat output.) > ************************************************************************** * * * Dr. Martyn Winn * * * * Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND * * Tel: +44 1925 603455 E-mail: [EMAIL PROTECTED] (personal) * * Fax: +44 1925 603825 E-mail: [EMAIL PROTECTED] (CCP4 problems) * * URL: http://www.ccp4.ac.uk/martyn/martyn.html * **************************************************************************
