[phenixbb] NCS restraints
Pavel Afonine
PAfonine at lbl.gov
Sun Feb 28 12:02:53 PST 2010
Hi Mirek,
refinement {
main {
ncs = True
}
ncs {
find_automatically = False
restraint_group {
reference = chain A and backbone
selection = chain B and backbone
selection = chain C and backbone
selection = chain D and backbone
coordinate_sigma = 0.01
b_factor_weight = 50
}
restraint_group {
reference = chain A and sidechain
selection = chain B and sidechain
selection = chain C and sidechain
selection = chain D and sidechain
coordinate_sigma = 0.05
b_factor_weight = 10
}
}
}
where:
- "ncs = True" tells phenix.refine to use NCS restraints during
refinement;
- "find_automatically = False" tells phenix.refine to use the NCS
groups definitions that you supplied, otherwise it will either define
them automatically from scratch (if nothing is supplied) or adjust user
defined selections if necessary;
- "coordinate_sigma" defines the strength of coordinate NCS restraints
(smaller the coordinate_sigma - stronger the restraints);
- "b_factor_weight" defines the strength of B-factor NCS restraints
(bigger the b_factor_weight - stronger the restraints).
Of course you can be more selective as shown in Maia's example. I will
improve phenix.refine manual on this subject.
Let me know if you have questions.
Pavel.
On 2/28/10 10:56 AM, Mirek Cygler wrote:
> Hi,
> I have NCS symmetry in my crystal and wouldlike to use it during the
> refinement. What is the strength of the restraints for the backbone, for the
> sidechains? How can I control these restraints?
> Thanks,
>
> Mirek
>
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