Incidentally, would it be possible to condense all of these options into the one place? In the regularisation/refinement dialog box that is linked off the model/fit/refine toolbar??? At the moment these controls seem to be scattered all over the place (and thus easy to miss if you're a 'newbie').
Cheers, Stephen 2009/7/16 Bernhard Lohkamp <[email protected]>: >> I'm working on a low resolution structure with less than ideal >> maps. In an attempt to restrain the Refine Zone command to take >> into account the geometry more I've tried playing with the >> 'set_matrix' keyword through the Python Scripting window. I've >> varied the value from 10-100, but the results of real space >> refinement are always the same (ie more often than not the residues >> are distorted beyond recognition in an attempt to fit them into the >> density). > > I doubt the refinements are the same. What kind of Chi2 do you get for > the different settings? > >> Combining Regularise Zone with Refine Zone doesn't help. >> It may improve the geometry, but it often undoes any previous >> fitting to the maps. >> Any suggestions? > > Have you tried torsion angle restraints? And secondary structure > restraints, Ramachandran restraints? Are planar peptide restraints > switched on? > > B > > *************************************************** > > Dr. Bernhard Lohkamp > Assistant Professor > Div. Molecular Structural Biology > Dept. of Medical Biochemistry and Biophysics (MBB) > Karolinska Institutet > S-17177 Stockholm > Sweden > > phone: (+46) 08-52487673 > fax: (+46) 08-327626 > email: [email protected] > -- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
