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
>
> [log in to unmask]
>
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