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Refinement: Difference between revisions
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=== R_free much higher than R === | === R_free much higher than R === | ||
=== how large should the difference between R_free and R be? === | === how large should the difference between R_free and R be? === | ||
For now, see [http://www.ncbi.nlm.nih.gov/pubmed/11937051 Kleywegt GJ, Jones TA."Homo crystallographicus--quo vadis?" Structure. 2002 Apr;10(4):465-72.] | |||
=== Wrong space group === | === Wrong space group === | ||
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This occurs most often at moderate resolution. However, [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0040099 the structure of the ketosteroid isomerase] had to be refined in P1 at atomic resolution, although it refines well in C2221 at lower resolution such as 1.5A. | This occurs most often at moderate resolution. However, [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0040099 the structure of the ketosteroid isomerase] had to be refined in P1 at atomic resolution, although it refines well in C2221 at lower resolution such as 1.5A. | ||
=== Refining low resolution structures === | |||
Maintaining the secondary structure of your model when refining against weak data can be really challenging. | |||
There are some options, but in the end you might have to accept a fairly large number of [[Ramachandran plot]] outliers. | |||
Try [[PHENIX|phenix.refine]] with the keyword "discard_psi_phi=False". Then the psi and phi dihedral angles should be restrained according to the CCP4 monomer library definitions. There was a [http://www.phenix-online.org/pipermail/phenixbb/2007-July/000357.html discussion of in in the phenixbb in juli 2007]. Also see the [http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19554.html discussion in the ccp4bb from december 2006]. | |||
Remember that [[Ramachandran plot|phi-psi angels]] are excellent for [[validation]] purposes, but only when they are unrestrained, so if you restrain them you lose this option! | |||
You can also try restraining alpha-helices hydrogen bonding, and beta-sheet cross-strand hydrogen bonds. This can be done in [[REFMAC]], [[PHENIX|phenix.refine]] and [[CNS]] (its documented for all of them). | |||
If you are really desperate, another option could be to use harmonic restraints in [[CNS]] to keep your backbone fairly fixed in parts of the map where you believe the secondary structure is correct (most likely alpha-helices). You could also fix main chain elements completely (in any refinement program), but it is definitely preferable to leave some room for change in the xyz-positions, and harmonic restrains are a nice way of doing exactly that. | |||