Pavel Afonine wrote:
Dear Ed,
Tightly restrained refinement will be equivalent to
torsion angle parametrization, since bonds and angles are essentially
fixed (but dihedrals are not).
Simply not true. Think why -:) Hint: in restrained refinement the weight
applies to all terms - bonds,
Pavel,
Simply not true. Think why -:) Hint: in restrained refinement the
weight applies to all terms - bonds, angles, torsions, etc... So if
you choose tight weight in such refinement the torsions will be
restrained as tightly as other terms (at least as it would be in CNS
or phenix.refine).
Pavel,
- In general you are free to decide what you name a domain: it can be
a residue, its part or the whole structure.
- What would be main and side for non-amino acid molecule, like a
whatever ligand?
I don't see how my freedom to explicitly define the terms I use in a
post is relevant.
Dear Ed,
Tightly restrained refinement will be equivalent to
torsion angle parametrization, since bonds and angles are essentially
fixed (but dihedrals are not).
Simply not true. Think why -:) Hint: in restrained refinement the weight
applies to all terms - bonds, angles, torsions, etc...
On Wednesday 03 February 2010 10:04:36 Pavel Afonine wrote:
I always suggest to run these refinement jobs and see which
one gives the best result:
1) TLS + individual isotropic ADP refinement (tls+individual_adp);
2) TLS + group individual ADP refinement (tls+group_adp);
I do not think
DISCLAIMER: When I say grouped B-factor refinement I mean CNS-style,
Bmain/Bside refinement. Not to be confused with more general domain
B-factor refinement where single B-factor is assigned to some part of
the structure.
Apart from improving data-to-parameters ratio, another argument for
Hi Ed,
DISCLAIMER: When I say grouped B-factor refinement I mean CNS-style,
Bmain/Bside refinement. Not to be confused with more general domain
B-factor refinement where single B-factor is assigned to some part of
the structure.
- In general you are free to decide what you name a domain:
Dear all,
I am refining a 3.1Å structure with Phenix.refine, using two ADP groups per
residue.
When doing refinement in Refmac, the way to go would be to tighten the
weights quite a bit to make up for the low resolution, resulting in small
deviations in bond lenghts and angles from the ideal
Jose Antonio,
I've seen similar behavior few years ago with grouped B-factor
refinement in CNS. The argument for the grouped refinement is as
follows:
This is better than individual B-factor refinement at low resolution
because you significantly reduce the number of parameters.
There are two
Hello,
1. The reduction in number of parameters is not that significant. On
average, you have some 8 atoms per residue, and thus 32 parameters with
individual B-factors (4 per atom). With grouped B-factors you have 26,
about 20% difference. While it sounds like a lot (hey, I just removed
Hi Jose Antonio Cuesta Seijo,
- at 3.1A I would try 1) refining individual isotropic ADPs, 2) combined
strategy of refining TLS+individual isotropic ADPs, 3) combined strategy
of refining TLS+group isotropic ADPs with one or two definable isotropic
B-factor per residue. Look at Rfree and
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