[phenixbb] heavy atom in pdb for refinement

Nathaniel Echols NEchols at lbl.gov
Fri Sep 11 16:08:59 PDT 2009

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
NEchols at lbl.gov

More information about the phenixbb mailing list