[phenixbb] Unknown atoms in refinement

Pavel Afonine PAfonine at lbl.gov
Wed Aug 22 12:37:38 PDT 2007


Hi Jeff,

here is the solution:

1) Rename your unknown amino acid from UNK to something like ZZZ (since 
UNK has special meaning);
2) Run elbow.builder to generate a cif file (stereochemistry 
definitions) for this unknown item:
% elbow.builder model.pdb --do-all
3) This will create a cif file  for ZZZ (the file you need named like 
elbow.model_pdb.all.001.cif, you can remove the other elbow output);
4) Run phenix.refine again specifying this cif file from the command line:
% phenix.refine model.pdb data.mtz elbow.enk_zzz_pdb.all.001.cif

If you have multiple unknown items, call them differently like ZZ1,ZZ2, 
... etc, so elbow.builder do not consider them as one single ligand.

Also, make sure you specify element type for each atom in unknown entry 
in your pdb file (column 78), so it looks like :
ATOM     32  CA  ZZZ A   5       3.055   1.059   3.693  1.00  
0.87           C
ATOM     33  CB  ZZZ A   5       3.965   0.435   2.634  1.00  
1.13           C
ATOM     34  CG  ZZZ A   5       3.531   0.603   1.177  1.00  
1.16           C
ATOM     35  CD1 ZZZ A   5       3.411   2.076   0.818  1.00  
1.88           C
ATOM     36  CD2 ZZZ A   5       4.502  -0.103   0.245  1.00  
1.67           C
ATOM     37  C   ZZZ A   5       1.634   0.527   3.541  1.00  
0.87           C
ATOM     38  N   ZZZ A   5       3.576   0.800   5.030  1.00  
0.92           N
ATOM     39  O   ZZZ A   5       1.246  -0.440   4.196  1.00  
1.23           O
ATOM     40  OXT ZZZ A   5       0.073   1.000   3.735  1.00  
1.11           O

Please let me know if you have any more questions.
Pavel.


Jeff Habel wrote:
>
> What's the best way of dealing with unknown atoms (UNK) in phenix.refine?
>
> I have a long disordered loop that runs basically the length of the 
> protein on the back side and there is a single "amino acid" in the 
> middle that I'm trying to model as UNK.  I can run a round of refmac 
> and auto generate a lib file with my ligand and the unk atoms but 
> phenix.refine balks at that with respect to the Van der Waals radii.
>
> Thanks for the help,
>
> -Jeff
>
>   
>
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