[phenixbb] editing geometry restraints for C-beta deviation

Pavel Afonine pafonine at lbl.gov
Fri Aug 17 21:30:47 PDT 2012

Hi Walter,

My suggestion would be to calculate OMIT map and construct alternative 
conformations based on it. At 1.1A resolution it either works or you 
don't have alternative conformations.
Also, validation criteria are statistical measures (mostly), and they 
tend to be tuned to most occurring cases based on data bases (PDB). So 
obviously deviations are possible and expected. As Ed pointed out 
already you should trust your 1.1A map, and OMIT map should help you get 
most of it.


On 8/17/12 8:07 AM, Walter R.P. Novak wrote:
> Hi,
> I have a relatively high-resolution (1.1 A) structure and one 
> threonine residue has a C-beta deviation outlier that I cannot prevent 
> via any traditional means. I would like to try to restrain the C-beta 
> deviation for this residue by scaling the geometry restraints for this 
> residue, but I am not sure of how I should define the restraint for 
> C-beta. Any suggestions are greatly appreciated.
> Thanks,
> Wally

More information about the phenixbb mailing list