[phenixbb] heavy atom in pdb for refinement

crystallogrphy qunwan1 at gmail.com
Fri Sep 11 16:28:07 PDT 2009


Actually, after I change Zn to ZN, phenix.elbow does not work with the
following error message:
phenix.elbow overall_best_090909e_001-coot-0.pdb --all-residues --do-all
 ------------------------------------------------------------------------------
  electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3
    - Nigel W. Moriarty (NWMoriarty at LBL.Gov)
 ------------------------------------------------------------------------------

 Random number seed:  1653885000
 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing
Parsing P

        No unknown residues
[qwan at phaser2 AutoBuild_run_10_]$ phenix.elbow
overall_best_090909e_001-coot-0.pdb
------------------------------------------------------------------------------
  electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3
    - Nigel W. Moriarty (NWMoriarty at LBL.Gov)
 ------------------------------------------------------------------------------

 Random number seed:  1654559024
 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing
Parsing P

        No molecule read

        Use --all-residues to view residues if this is a PDB file


On Fri, Sep 11, 2009 at 7:19 PM, Pavel Afonine <PAfonine at lbl.gov> wrote:

>  Yes, the capitalization matters. Ralf is notified.
> Pavel.
>
>
>
> On 9/11/09 4:08 PM, Nathaniel Echols wrote:
>
> On Sep 11, 2009, at 3:54 PM, Pavel Afonine wrote:
>
>
>  I have Zn atoms in my pdb for refinement. However, it failed with
> the following scripts. Do I have to create a libary of this heavy
> atom?
>
>
>  no, you shouldn't. Zn should be recognized automatically if it is
> properly defined in input PDB file. I just verified that if it is
> formatted like this:
>
> HETATM 2306 ZN    ZN D   1      24.598  75.945  -1.390  1.00
> 5.00          ZN
>
> then it works fine. I'm not sure if capitalization is important as
> well as HETATM instead of ATOM - this is something you can try in no
> time.
>
>
>
>
> I'm pretty sure capitalization is indeed important, because I had a
> similar problem in both phenix.refine and eLBOW with manganese (MN is
> okay, Mn is not).
>
> -------------------
> Nathaniel Echols
> Lawrence Berkeley Lab
> 510-486-5136NEchols at lbl.gov
>
>
>
>
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