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Refinement: Difference between revisions
→Refining low resolution structures
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=== Refining low resolution structures === | === Refining low resolution structures === | ||
Maintaining the secondary structure of your model when refining against weak data can be really challenging. | Maintaining the secondary structure of your model when refining against weak data can be really challenging. When building manually, you may end up with 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 it in the phenixbb in July 2007]. Also see the [http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19554.html discussion in the ccp4bb from December 2006]. | 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 it in the phenixbb in July 2007]. Also see the [http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19554.html discussion in the ccp4bb from December 2006]. | ||
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Remember that [[Ramachandran plot|phi-psi angles]] are excellent for [[validation]] purposes but only when they are unrestrained. If you restrain them, you lose this option! | Remember that [[Ramachandran plot|phi-psi angles]] are excellent for [[validation]] purposes but only when they are unrestrained. 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]] | You can also try restraining alpha-helices hydrogen bonding, and beta-sheet cross-strand hydrogen bonds. This can be done in [[REFMAC]] (using ProSMART) and [[PHENIX|phenix.refine]] (using a reference model). | ||
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 restraints are a nice way of doing exactly that. | 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 restraints are a nice way of doing exactly that. | ||