[phenixbb] ramachanran plot refinement or restraint?

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Thu Jul 26 01:36:22 PDT 2007

Hi Jianghai

For that, you have to rebuild your model.  Ramachandran outliers are 
symptoms of poor model, so you have to fix it by hand.  Even if it is 
low resolution and huge.

ESPECIALLY if it is low resolution and huge.


For the hugeness issue, DEFINITELY use tight NCS restraints if you have 
higher NCS.  a) it means less building, and b) it makes refinement more 

Also, please refer to Tassos email on ccp4BB this week:  the question 
implies you have some basic reading to catch up on, about refinement and 
rebuilding in general.


Jianghai Zhu wrote:
> Hi,
> I am refining a low resolution huge protein structure.  There are about 
> 20% residues in the disallowed region of ramachandran plot.  Is there a 
> way in phenix.refine to refine the phi, psi angles to get a better 
> ramachandran plot?  or a phi, psi restraints in refinement?
> Thanks.
> Jianghai
> +++++++++++++++++++++++++++++++
> Jianghai Zhu, Ph.D
> CBR Institute for Biomedical Research
> Department of Pathology
> Harvard Medical School
> 200 Longwood Ave., Boston, MA 02115
> Ph: 617-278-3211
> Fx: 618-278-3232
> +++++++++++++++++++++++++++++++
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