Dear All, 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. In addition, for Coot and Ming, which is much convenient to reduce rotamer outlier? I am looking forward to getting your reply. Cheers, Fenghui
On Sat, Dec 3, 2011 at 3:00 AM, Dialing Pretty
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
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
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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Sat, Dec 3, 2011 at 2:10 PM, 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/
Oh, did you mean "KiNG"?
Will you please also introduce me a webpage based on which I can reduce my rotamer outlier (currently 8% by Phenix evaluation).
The tutorials at that URL are the best introduction I know of.
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?
They're purely statistical - the fifth citation on that page ("The penultimate rotamer library") gives details. The validation in PHENIX does calculate fit to the electron density, but this is done separately. -Nat
participants (2)
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Dialing Pretty -
Nathaniel Echols