[phenixbb] heavy atom in pdb for refinement

Pavel Afonine PAfonine at lbl.gov
Fri Sep 11 16:19:45 PDT 2009


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
> 510-486-5136
> NEchols at lbl.gov
>
>
>
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>   
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