On Tuesday 10 August 2010 10:30:17 am Sue Roberts wrote: > Hello Everyone > > There's probably an easy way to do this, but I haven't found it. > > I've refined a 1.1 A structure with refmac and want to inspect the thermal > ellipsoids. Specifically I want to know if any of them are non-positive > definite and I want to know which have very large anisotropy. (I can look at > them in coot, but I'd like to have a list).
The Parvati server was designed for exactly this purpose. It is a validation tool for anisotropic refinement, and may help you to adjust the restraint weights used during refinement, particularly if your resolution is not quite at that ultra-ultra-high <1A range. http://www.bmsc.washington.edu/parvati/ We have recently extended the Parvati validation test suite for use with anisotropic models refined using TLS rather than individual ellipsoids. And yes, there is an updated version of TLSANL to go with it but I think it has not escaped into the wild yet. Frank Zucker, P. Christoph Champ and Ethan A. Merritt Validation of crystallographic models containing TLS or other descriptions of anisotropy. Acta Cryst. (2010). D66, 889–900 cheers, Ethan > I'm concerned because I get messages in the refmac log file - problem with > make u positive and I want to know what the cause of the error messages. > > I thought anisoanl would be the most likely program, but it doesn't seem to > do it. (Perhaps I'm using the program wrongly.) > > Thanks > > Sue > > Dr. Sue A. Roberts > Dept. of Chemistry and Biochemistry > University of Arizona > 1041 E. Lowell St., Tucson, AZ 85721 > Phone: 520 621 8171 > s...@email.arizona.edu > http://www.biochem.arizona.edu/xray > -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
