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 ([email protected])
------------------------------------------------------------------------------
Random number seed: 1653885000
0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing
Parsing P
No unknown residues
[qwan@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 ([email protected])
------------------------------------------------------------------------------
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
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 [email protected]
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