On Mon, Dec 5, 2011 at 2:48 AM, Dialing Pretty
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?
This sounds like the classic "exploding hydrogens" problem. You should update to the latest version of Coot (possibly one of the nightly builds), which has the new hydrogen definitions which are more compatible with Phenix.
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?
We can't answer this accurately without knowing more about what atoms it complains about. Normally this indicates that restraints are missing, but it's possible this is related to the problem with hydrogen atoms. -Nat