[phenixbb] the Ming dial

[Dialing Pretty]

Dear All and Nat,
 
The Ming webpage is following, which I am also in the learning process.
 
 
http://kinemage.biochem.duke.edu/teaching/workshop/MolProbity/
 
Will you please also introduce  me a webpage based on which I can reduce my rotamer outlier (currently 8% by Phenix evaluation).
 
In addition here I have a basic concept which I am confused:
 
The outlier here (for rotamer) analyzed by Phenix evalutation is defined by that the outlier rotamer conformaton does not comply with the statstics of the rotamer conformation of that residue in the published PDB, or it is because the so-called rotamer outlier is caused by its the outlier rotamer conformation does not comply with the electronic density map?
 
I am looking forward to getting a reply from you.
 
Cheers,
 
Dialing

________________________________
From: Nathaniel Echols <nechols at lbl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org> 
Sent: Sunday, 4 December 2011 4:56 AM
Subject: Re: [phenixbb] the Ming dial

On Sat, Dec 3, 2011 at 3:00 AM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> In the Ming dial, there is a occupancy (%), which indication of excellent ,
> good, etc. Does it mean if I choose the "occupancy" of excellent, the
> rotamer outlier ratio will be lowered? My crystal has a resolution of 2.8,
> and I find no matter how I turn the dial, the original fits the map best.
> Currently my rotamer outlier is 8%, thus I need the way to have it solved.

I'm not familiar with the program Ming - can you point us to a web page?

Regarding rotamer outliers, it may be difficult to completely
eliminate them at this resolution - the dihedral angle restraints are
not very tight.  However, you may need to adjust the backbone to get a
rotameric sidechain conformation to fit the density properly (before
and after refinement).

-Nat
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