It would be possible to model all of that with SHELXL, but it is a complex problem and would need time and patience with any program. One advantage of SHELXL would be the flexible refinement of occupancies for the different conformations.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 27 Feb 2009, Michael Weyand wrote: > Dear experts, > > here is a Refmac question (or at least a refinement question): > > the case: data set was collected at the synchrotron with high intensity or > better high total dose. Data set scales to 1.2A resolution. > Refinement with refmac5_0066, using hydrogens, anisotropic B-factors, > automatic weight (actually 17.9), 235 amino acids, approx. 450 waters, > several ions and buffer/crystallization compounds, a hell of second and third > side chain conformations, present R-fac 12.6, free-R 15.6. > > I think I'm seeing a (partial) backbone break (negative DelFwt density for > backbone atoms at 3.5sig within coot) due to radiation damage in a surface > loop. I see clear missing COOH- and Guanidinium-groups in other parts of the > model!! > > As a consequence, the protein adopts a second (backbone) conformation (clear > positive DelFwt at 4.0sig) for an alpha-helix. But some of the second > conformation residues are not visible. > Summary: > conformation A (aa206-219) ~ 70% occupancy, > conformation B (aa212-219) ~ 30% occupancy, no density (flexibility??? / > deletion ???) for aa206-211. > > Refmac always link aa212, conformation B to aa211, conformation A. But, the > CA distance between Calpha atoms of aa212 is / should be about 5A. > > How to address the "non-restraint" between these amino acids, or vice versa > to address a (partial) chain break? > > Furthermore I see "partial" waters at a (second) side chain > conformation/position. Is it also possible to release the restraints for > these waters to atoms of the second side conformation? > > It is really important to do it right, since the second conformation residues > change the active site with a bound ligand. > > Every hint or work-around is highly appreciated. > May be I have to use SHELXL? > > Regards > Michael > > > > -- > Dr. Michael Weyand mail: michael.wey...@mpi-dortmund.mpg.de > Max-Planck-Institut fuer molekulare Physiologie, Otto-Hahn-Strasse 11 > D-44227 Dortmund, Germany, fon: +49(0)231-133-2738, fax: +49(0)231-133-2797 >
