[phenixbb] editing geometry restraints for C-beta deviation

Edwin Pozharski epozh001 at umaryland.edu
Fri Aug 17 08:26:09 PDT 2012


could this be done by editing the .geo file, which contains all the 
restraints?  It's in text format and thus easy to interpret.  A 
workaround could certainly be to rename the threonine to a new amino 
acid type with correspondingly tightened geometry parameters.

On the other hand, maybe you should trust your very high resolution 
data.  At 1.1A, unrestrained refinement is definitely possible and if 
the electron density suggests the geometry is distorted, perhaps it is.



On 08/17/2012 11:07 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

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