[phenixbb] rotamer outlier reduction by coot

Dialing Pretty hdc123hdc123 at yahoo.com
Mon Dec 5 02:48:14 PST 2011

Dear All,
I am leaning rotamer outlier reduction by Coot. 
After select a rotamer and acception, I find some hydrogens in the outlier rotamer will be isolated from the rotamer, and the rotamer will have new hydrogens at its new position. Is any influence by further refine by phenix?
After new rotamer acception, I have did the rotamer auto-fit, I find there is a trend on that several oxygens can pack together. How to process this problem?
After I save the new PDB file by coot after I selected the new rotamers to replace the outlier rotamers, I did a Phenix refine. There is an error message at the start says "Number of atoms with unknown nonbonded energy typensymbol: 2228". What does it mean and how to solve the problem?
Is any simple method by which I can do the rotamer outlier reduction by Coot? 
I am looking forward to getting your reply.
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