There are a number of things that don't look right here, both with the
Refmac and the Phenix runs:
1. The Refmac T22 looks too small compared with T11 & T33, unless it
really is highly anisotropic, but this would be unusual!
Alternatively the elements of T (& possibly L) somehow got in the
wrong order. The order expected (see doc) is 11 22 33 12 13 23.
The same goes for the elements of L; also check the doc for the order
of S.
2. The COR for Phenix is clearly garbage, probably because the L & S
elements are much too small. It looks like you've given the values in
SI units (aka radians) whereas Refmac & TLSANL expects multiples of
degree^2 for L and degree for S, where 1 degree = pi/180 & therefore 1
degree^2 = (pi/180)^2. Sorry, I know we should be using SI but I find
I can't easily comprehend the numbers because either they have lots of
leading zeros or they have to be printed in floating point format.
Also you're losing a lot of significance in the Phenix L values - they
have only 1 sig figs!
I agree the conventions are arbitrary for all of this but at least
they are defined unambiguously in the REFMAC & TLSANL documentation
(and I assume also the Phenix documentation!). S should not have been
symmetrized (if it were it would have only 5 unique elements instead
of the 8 it appears to have); instead the elements are defined
uniquely by the given origin, the co-ordinate reference frame and by
the condition trace(S)=0 (which is why you have 8 elements & not 9).
-- Ian
On Thu, Oct 21, 2010 at 3:55 PM, Bryan Lepore <bryanlep...@gmail.com> wrote:
>> documentation
>
> then i conclude the TLS protocol in refmac is markedly different from
> phenix (i know this is not strictly a ccp4 question). cf. :
>
> refmac:
> TLS
> RANGE 'A 245.' 'A 252.' ALL
> ORIGIN 14.019 -10.476 -35.068
> T 0.4974 0.0372 0.3453 0.0674 0.2984 0.0431
> L 21.5463 29.5753 20.7545 39.3304 9.2958 -11.5975
> S 0.6432 1.0787 -0.1449 1.2672 2.1065 1.5489 -1.1854 -0.0349
> center of reaction : 18.652 -5.646 -40.945 from orth. axes
> libration perpendicular to TLS plane : 13.256 deg^2
>
> phenix:
> TLS
> RANGE 'A 245.' 'A 252.' ALL
> ORIGIN 14.019 -10.476 -35.068
> T 0.2961 0.2533 0.2969 -0.0097 0.0111 0.0205
> L 0.0006 0.0005 0.0006 0.0006 -0.0002 -0.0001
> S 0.0058 -0.0026 -0.0027 0.0035 -0.0017 0.0011 -0.0052 0.0027
> center of reaction : -606.636-734.593 -54.324 from orth. axes
> libration perpendicular to TLS plane : 0.001 deg^2
>
> .... (trying to keep this a refmac/tlsanl question) and the results
> are equivalent - because of factors perhaps in symmetrization of S,
> because there are no unique choices of these things. if so, only the
> refmac axes faciliate an intuitive comparison.
>
> regards,
>
> -bryan
>
> p.s: link to original thread phenix board :
>
> http://www.phenix-online.org/pipermail/phenixbb/2010-October/004724.html
>
