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On Tue, 22 Aug 2006, Mario Sanches 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 on the final stage of refinement and I am making sure, on coot, > that the residues are in the allowed regions of the Ramachandran Plot. > The problem is that, after Refmac, those residues are thrown back on the > disallowed regions. > > This a low resolution structure (3.35A). I am using a matrix weight > which renders a RMSD bond of 0.02A. Since it is very low resolution, I > thought it would be a good idea to keep all residues in the allowed > regions. Is there any way to tell Refmac to keep it there? > > Thank you in advance, > > Mario Sanches Hi, I know that I'm not answering your question, however I noticed something weird about the use of Refmac you mention: at the resolution you're working at (I suppose given by your crystals, not by choice I assume) the RMSD on bond lengths should be ca. 0.012, not 0.02 A. Thus my guess is that the geometry is poorly restrained, too much weight given on the X-ray term during refinement. Perhaps you should adjust the weight so that the geometry is restrained more tightly and see how it goes. Fred. -- s-mail: F.M.D. Vellieux (B.Sc., Ph.D.) Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: (+33) (0) 438789605 Fax: (+33) (0) 438785494 e-mail: [EMAIL PROTECTED]
