On Tuesday 26 June 2007 10:43, Sue Roberts wrote: > Hello Everyone > > This isn't really a question, just a warning to check your > anisotropic temperature factors both after refinement and after > deposition at the pdb.
I encourage everyone who is refining, depositing, or inspecting structures with anisotropic ADPs to validate them using the Parvati web server: http://skuld.bmsc.washington.edu/parvati/parvati.html (If it mis-handles these apparently totally messed-up files that Sue refers to, please let me know) Ethan > We've been having a lot of trouble with anisotropic temperature > factors lately. Here's what's been going on. > > We have three different proteins, each diffracting better than 1.2 A > - the best resolution is ~ 0.8 A. All have been refined with refmac > (yes I know shelxl is great for such problems, but that's not the > issue here). > > For structures refined with some versions of refmac (including the > ccp4-6.0.2 linux distribution from early this year), the anisotropic > components output on the ANISOU card are ridiculous. When we run > anisoanl, ALL atoms are flagged as non-positive definite. When I ask > coot to show anisotropic ellipsoids, they have only two dimensions > (coot doesn't crash, Paul has the negative numbers trapped). > Refinement of the same data set/coordinates with shelxl produces > anisotropic temperature factors which are reasonable as judged by > these two methods. I can "fix" the refmac "problem" by installing > the latest version of refmac from Garib's web page (not the version > in ccp4-6.0.2). The anisotropic ellipsoids are now good (as judged > by anisoanl and coot). (Repeating myself, these are all very high > resolution structures). > > So, I thought the problem was solved. > > We reviewed structures we'd deposited with the pdb but were as yet > unreleased and found one with unrealistic thermal ellipsoids, which > confused us since the depositor had done the sanity checks before > depositing the coordinates. > > When we compared the file we submitted to the pdb and the file which > was returned to us, the numbers on ALL the ANISOU cards had been > rotated in this fashion: > > ANISOU 1 N MET A 1 1612 1818 1492 2 -160 > -14 A N > > has become > > ANISOU 1 N MET A 1 1612 2 -14 1818 1492 > -160 N > > In other words the aniso card, (u11,u22,u33,u12,u13,u23) > has been rearranged to be (u11,u12,u23,u22,u33,u13) (this doesn't > make any sense to me) > > I can speculate that the refmac/pdb issues are interlinked and one > arises from an attempt to fix the other, but I don't know that that's > true. I did a quick check of structures released by the pdb in the > last year with resolution > 1.1 A and found at least one with the > same problems (I stopped looking after I'd found one). > > Sue > > Sue Roberts > Biochemistry & Biopphysics > University of Arizona > > [EMAIL PROTECTED] > -- Ethan A Merritt Courier Deliveries: 1959 NE Pacific Dept of Biochemistry Health Sciences Building University of Washington - Seattle WA 98195-7742
