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You can either generate a pseudo-noe-file for your SS-elements and
incorporate that as additional restraints.
What I did is to use a modified NMR-script (for X-plor that was, but
most of it works with CNS though I remember at least one key-word was
not documented in CNS) and refine against an additional Ramachandran
potential. It proved very useful in one case of medium/low resolution
(<3A ) and didn't improve things in two others.
There are several problems with this approach that you have to be aware of.
- The potentials are derived from Procheck, so all problems with the
Procheck-Ramachandran plot apply (see older thread).
- Assessing what is 'improve' is not so easy. What I did was to lower
the weight for the X-ray term to 1/100000 of its original value. Like
that it does not influence the refinement but R-factors are still
computed. A simulated annealing in this force field lowered R-free by
several percent-points, which lead me to believe in this case the
refinement was stuck in a local minimum and the application of
Ramachandran-constraints (or is it restraints) helped to push it out of
there.
- You bias your structure to have a 'good' Ramachandran, so this
analysis won't tell you the quality of your structure. Several
additional rounds of refinement w/o Rama-restraints did not destroy the
good geometry, the Ramachandran plot of this structure is not a measure
of its quality/correctness.
If you want to give it a try anyways, I'll dig through my hard drive and
find those scripts.
HTH
Jens
abdul azeez wrote:
Hi
I wish to maintain secondary structures during the refinement using
the knowledge from
previously solved structure.
Is there any way to keep helices and antiparallel beta sheets as such
during the refinement
using Refmac / CNS.
If yes, then what is the procedure to do that. And what are limits I
have to use to retain the
secondary structures.
Thanking you in advance.
Abdul Azeez
Postdoc, CBSE, UAB, USA.
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