[phenixbb] Limit Ramachandran restrain to certain region

Nian Huang huangnian at gmail.com
Wed Apr 4 00:57:10 PDT 2012

I was using 1.6.1. Now I am trying 1.7.3 now to see if it will fix my
problem. I actually used ramachandra restrain in coot during building
those loops, but some residues still changed back. That's why I was
considering for this option. Thanks.


On Tue, Apr 3, 2012 at 3:47 PM, Nathaniel Echols <nechols at lbl.gov> wrote:
> On Tue, Apr 3, 2012 at 1:38 PM, Nian Huang <huangnian at gmail.com> wrote:
>> Is it possible to limit Ramachandran restrain to specified residues in
>> phenix.refine? I have a couple of loops with very poor density. The
>> refinement process always made some residues fall out of ramachandran
>> plot no matter how I tightened the weight and adjusted the residues
>> back. Because the diffraction is about 2.3 A, I don't want the
>> ramachandran restrain to impact the rest of structure. Thanks.
> Which version of Phenix are you using?  If it's 1.7.1 or earlier, you
> need to update to the latest version ASAP, because this will probably
> fix the problem.
> If you're already using the latest version, the parameter
> rama_selection will do what you want.  But you really shouldn't need
> Ramachandran restraints at 2.3A resolution - and I'd advise against
> using them entirely, at any resolution.  They're just too dangerous
> and lead to unnatural structures.  You also probably don't want to be
> running real-space refinement for this structure.  However, when
> you're rebuilding, using Coot's Ramachandran restraints together with
> its local real-space refinement should be sufficient to give you a
> good starting model, which Phenix will hopefully not screw up.
> -Nat
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