question about constrain ncs
Hi, I am refining a 3.6A data set. There are 5 monomers per asymetric unit. I am considering to use constrained NCS to increase the ratio of reflection/parameter. Does phenix.refine has a script to put contrained ncs or I just use simple_ncs_from_pdb to determine the best NCS?
Hi, phenix.refine model.pdb data.mtz main.ncs=true will do refinement with NCS restraints. The NCS groups will be determined automatically. It may be important to check the automatic choice. See phenix.refine manual for details: http://phenix-online.org/documentation/refinement.htm#anch24 Also, at this resolution you may consider using TLS and/or group ADP refinement. phenix.refine does not have NCS constrains, which I believe you do not need at this resolution. Pavel. On 10/1/09 8:33 PM, crystallogrphy wrote:
Hi, I am refining a 3.6A data set. There are 5 monomers per asymetric unit. I am considering to use constrained NCS to increase the ratio of reflection/parameter. Does phenix.refine has a script to put contrained ncs or I just use simple_ncs_from_pdb to determine the best NCS? ------------------------------------------------------------------------
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Hi Jon, try this: - run phenix.refine with NCS restraints and use "optimize_wxc=true" (just out of curiosity, try w/o this option). Try these strategies to see which one works best: "strategy=individual_sites+group_adp+tls" or "strategy=individual_sites+individual_adp+tls" (don't forget to specify TLS groups. How? It is a separate question). - run CNS or Refmac (whatever you like) using NCS constraints. Compare Rwork, Rfree and Rfree-Rwork, map CC for each residue (phenix.real_space_correlation), and then you have a conclusive answer. Everything else are speculations -:) Answering your question - yes, NCS constraints are in (my ?) to-do list. I would appreciate if you share the results of the above experiment with me. And I'm open for further discussion. All the best! Pavel. On 10/6/09 6:55 AM, Jonathan Grimes wrote:
Pavel Afonine wrote:
Hi,
phenix.refine model.pdb data.mtz main.ncs=true
will do refinement with NCS restraints. The NCS groups will be determined automatically. It may be important to check the automatic choice. See phenix.refine manual for details: http://phenix-online.org/documentation/refinement.htm#anch24
Also, at this resolution you may consider using TLS and/or group ADP refinement.
phenix.refine does not have NCS constrains, which I believe you do not need at this resolution.
Pavel.
Hi Pavel,
Got to disagree with you on this one. Depends on your obs to params. If youve got 90% solvent then perhaps.......I would always favour reducing my params by a factor of 5 at 3.6Angs.
Jon
PS Any plans for coding up NCS constraints !!! ;-)
-- Dr. Jonathan M. Grimes, University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK
Email: [email protected], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
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participants (3)
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crystallogrphy -
Jonathan Grimes -
Pavel Afonine