[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.
Sux.
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
robust.
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.
Cheers
phx
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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