[phenixbb] ncs

Pavel Afonine PAfonine at lbl.gov
Sat Jun 27 10:28:14 PDT 2009

Hi Maia,

> I made all restraint_groups in my parameter file. It's just too many of 
> them. I thought that may be there is an option to say exclude residues 
> 125, 248 etc. 

No - there is no such command: you need to edit selections manually.

> By the way, I have  excessive_distance_limit = None. If I 
> change it to some number, how does it work? the violating residues will 
> be  excluded or the whole molecule will?

I'm not sure, Ralf knows this better. Ralf, could you comment on this 

My guess, that all this parameter does is it checks the distances 
between atoms in NCS copies and if there is a distance larger than 
excessive_distance_limit, then phenix.refine stops and tells you this.


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