[phenixbb] questions

Jianghai Zhu jzhu at cbr.med.harvard.edu
Wed Dec 13 19:00:32 PST 2006


Got some questions in using phenix.refine.

1) Can phenix.refine use the ligand library generated by refmac5?

2) How do I use elbow to generate the ligand library when I have more  
than one kind of ligands?  When I used --residue=xxx more than once,  
elbow will only generated library for the last ligand.  If I use  
elbow multiple times to generate multiple libraries, how do I read  
the libraries in?  Should I combine them to one file?

3) When I ran phenix.refine, I found the following message in the log.

         Number of residues, atoms: 32, 418
           Unusual residues: {'NAG': 22, 'MAN': 10}
           Classifications: {'undetermined': 32}
           Link IDs: {None: 31}
           Unresolved non-hydrogen bonds: 32
           Unresolved non-hydrogen angles: 64
           Unresolved non-hydrogen dihedrals: 22
           Unresolved non-hydrogen chiralities: 32
         Number of residues, atoms: 18, 28
           Unusual residues: {'GOL': 2, ' MG': 2, ' CA': 14}
           Classifications: {'undetermined': 18}
           Link IDs: {None: 17}

I already gave the cif library for NAG.  Looks like nothing  
happened.  How come phenix.refine doesn't recognize Glycerol, Mg, and  

4) The refinement (TLS + ML + B individual) went through, I got  
reasonable R, Rfree, rmsdBOND, rmsdANGLE.  But the B factors are  
pretty low.  The B factor of the backbone is much lower than the side  
chain, some have numbers like 4.  Some metal atoms also have B  
factors around 4.  What did I do wrong?



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