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Eleanor Dodson wrote:
All this is prob. true, but I repeat -
should tight default stereochemistry be a requirement at the early
stages of refinement at reso > 2.5A anyay?
Eleanor
Good question - I usually tell our PhD students to have tight geometry
(rmsd bonds between 0.012-0.015 A) at the end of the refinement run,
hoping that this reduces overfitting and model bias by at least some
extend. But your question reminds me of a different refinement protocol,
recommended in an older TNT manual: first, refine with high weights on
the X-ray term to allow larger shifts with poor stereochemistry, then do
more refinement with lower weights on the X-ray term to tighten the
geometry, again. This scheme is probably almost forgotten, but should
still be useful! A complementary approach would be to start refinement
with high weights on the X-ray term AND lower maximum resolution to
allow a larger radius of convergence, and then include higher resolution
data and tighten your geometry. This is quite labour-intensive. If I
remember correctly, BUSTER/TNT does a smooth effective resolution
limitation dependent on the quality of the fit of the model to the data
by including several sources of variances in a Luzzati-type of scaling.
As the model improves during refinement and the total variance
decreases, the effective resolution apporaches the resolution limit of
the observed data. I think, this is very elegant and should be an option
in every modern refinement package.
Best regards,
Dirk.
Anthony Duff wrote:
In my opinion...
CNS seems superior for low resolution structures (resolution worse
than 3A) and early refinement (R worse than 30%). Reasons:
* good radius of convergence,
* tight default stereochemistry,
* very easy to use with a simple model
* simulated annealing
* ability to refine part only of the model
* ability to use harmonic restraints,
* ability to not refine B-factors,
* ability to only refine B-factors
Otherwise REFMAC is superior:
* more aggressive minimisation algorithm.
* very easy to use alternate conformers
* Ongoing development
* excellent community support for when things get tricky (ccp4bb)
I suggest that the best transition point is where you need to model
alternate conformers. Once you have your first alternate conformer,
abandon CNS and use REFMAC from that point forward.
Anthony
At 08:57 AM 7/12/2005, you wrote:
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Dear all,
My model (total 354 residues) has 13 residues which have alternate
conformations. when I generate the alternate conformation with
alternate.inp in CNS, the program does not give me the AC conformers
because the atom selection only allows for 265 letter. However, all
these residue selection will more than 264 strings. Does any one
know how to the alternates in CNS?
DEFINE>{========================== atom selection
===========================}
DEFINE>
DEFINE>{* select atoms to have multiple conformations *}
%COPYST-ERR: ST2MAX too small. Check input file.
Offending string:"{===>} atom_select=((segid A and
residue 12) or (segid A and residue 169) or (segid A and residue
175) or (segid A and residue 172) or (segid A and residue 37) or
(segid A and residue 222) or (segid A and residue 126) or (segid A
and residue 51) or (segid A and re "
with length= 265
Max allowed length of string= 264
----------------------------------------------------------------------
Anthony Duff
Postdoctoral Fellow
School of Molecular and Microbial Biosciences
Biochemistry Building, G08
University of Sydney, NSW 2006 Australia
Phone. 61-2-9351-3907 Fax. 61-2-9351-4726
----------------------------------------------------------------------
--
****************************************
Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
****************************************
