[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

  - "ncs = True" tells phenix.refine to use NCS restraints during 
  - "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.

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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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