[phenixbb] questions

Nigel W. Moriarty nwmoriarty at lbl.gov
Thu Dec 14 08:58:56 PST 2006


I can answer some of your questions. See below.

Jianghai Zhu wrote:

>Got some questions in using phenix.refine.
>1) Can phenix.refine use the ligand library generated by refmac5?
Yes, it should.

>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?
If you have a more recent version of eLBOW you can create a single 
restraints file for a single PDB file thus

elbow.builder protein_and_ligands.pdb --do-all --opt

In older versions, you should be able to

elbow.builder protein_and_ligands.pdb --residue=LG1,LG2,LG3 --opt

to generate the residues you desire.  Use


to combine single CIF files into one file.

To read more than one CIF file into phenix.refine simply add the file 
names to the command line

phenix.refine filename.pdb filename.mtz ligand1.cif ligand2.cif

>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  
The most recent version of phenix.refine will recognise the single metal 
atoms but currently you need to generate the CIF for glycerol with 
eLBOW.  I have attached a CIF file for GOL using the standard atomic 
naming from the PDB MSDChem database.

>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?
>phenixbb mailing list
>phenixbb at phenix-online.org

Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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