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On Wednesday 30 August 2006 06:39, xiaoyazi chen wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hi, everyone, > > I am working on refinement of 3.8A data. The structure was solved by > molecular replacement with phaser. The crystal belongs to spacegroup P43 > with 2 copies of complex in ASU. Each complex contains four domains. It > seems that the MR solutions are correct, because it gave reasonable Z > scores (6.0, 10.8, 12.7, 11.3, 15.9, 14.3) for the six domains. It is very > difficult to find the last two small domains. So I just did rigid body > refinement and annealing, manually placed the remained two domains > according to the fo-fc map. Based on this solution, I performed the > refinement with refmac5, but the Rf and R (48%, 43%) are quite high. > > Are there any suggestions on searching the lost domains and refinement on > such low resolution data. It depends on what you might know about the relative orientation of these domains to the rest of the structure. If both domains are present in the model (covalently or non-covalently associated) and you expect a similar relative orientation to what you see in the model, then you can concentrate on similar orientations using the ROTATE AROUND command, allowing (say) 10-30 degrees difference in orientation. If not, it might help to use a more exhaustive search of orientations for the two copies of the small domain, using for example SAVE ROTATION SELECT PERCENT 60. The rotation signal can be quite small for a small component, so that you don't get a good peak, but the translation search can pull out the correct orientation. -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [EMAIL PROTECTED] Cambridge CB2 2XY, U.K. www-structmed.cimr.cam.ac.uk
