On Monday, 20 October, 2014 18:10:03 Appu kumar wrote:
> Dear CCP4 Users,
> I seek your valuable advice and suggestion in carrying out the normal mode
> structure refinement which manifest the dynamics of protein as linear
> combination of harmonic modes, used to describe the motion of protein
> structure in collective fashion. Studies suggest that it is highly useful
> in refining the protein structure which harbors a considerable magnitude of
> flexibility in atomic position owing to high thermal factors.
> Therefor I want to know is there any software/script available to execute
> the normal mode of refinement. Thanks a lot in advance for your imperative
> suggestions
The previously published examples of normal-mode refinement that I know
about used private external programs to generate thermal ellipsoids for each
atom, and then used those as fixed ADPs while refining coordinates in
refmac or similar standard program. Again speaking only of the examples
I have looked at in detail, the result was "better" (had lower R factors)
than a conventional isotropic refinement but was not nearly as good as a
multi-group TLS refinement of the same structure (TLSMD + refmac).
On the other hand, there is a quite different way normal modes can be used
in refinement. As I understand it (perhaps Garib will add addtional details)
the "jellybody" refinement mode of recent refmac versions can be viewed
as restraining the model shifts to be consistent with the principle normal mode.
In this way the normal mode contributes to the path of the refinement,
but is not explicitly part of the final model.
So it may be that using TLSMD + refmac jellybody TLS refinement
would get you the best of both approaches, though I have not gone back
to look again at the published example structures since the advent of
jellybody refinement. But note that jellybody is primarily useful when
you already have a high-qualityl, good geometry, starting model.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
