Refinement: Difference between revisions

20 bytes removed ,  25 May 2018
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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.
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 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]], [[PHENIX|phenix.refine]] and [[CNS]] (it's documented for all of them).  
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.
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