[phenixbb] creating cif for Zn

Pavel Afonine PAfonine at lbl.gov
Tue May 26 13:58:40 PDT 2009


Hi Raja,

this should work (the rightmost Zn is shifted one space left as required 
by PDB format):

ATOM      1  Zn   Zn A   1       1.059  -1.211 -15.432  1.00 
16.89          Zn

let me know if it doesn't.

Pavel.


On 5/26/09 1:52 PM, Raja Dey wrote:
> Hi Pavel,
> I enclosed the line below:
>
> ATOM      1  Zn   Zn A   1       1.059  -1.211 -15.432  1.00 16.89      A    Z
>
> I also tried with 
>
> ATOM      1  Zn   Zn A   1       1.059  -1.211 -15.432  1.00 16.89      A    Zn
>
> None worked.
>
> Raja 
> ----- Original Message -----
> From: Pavel Afonine <PAfonine at lbl.gov>
> Date: Tuesday, May 26, 2009 12:40 pm
> Subject: Re: [phenixbb] creating cif for Zn
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
>
>   
>> Hi Raja,
>>
>> normally phenix.refine should recognize Zn atoms without any 
>> problems 
>> and you don't need run elbow for this. If it doesn't, that most 
>> likely 
>> means your PDB file is ill-formatted (for example, no element type 
>> defined in 77(?) column). Could you please send me copy of the ATOM 
>> line 
>> from your PDB file containing Zn so I can tell what is wrong?
>>
>> Pavel.
>>
>>
>> On 5/26/09 12:31 PM, Raja Dey wrote:
>>     
>>> Dear Friends,
>>>                      I have Zn atoms in my pdb file. So, I think 
>>>       
>> I need to run elbow to create the cif  otherwise refinement stops.
>>     
>>> I did the following and got the error as follows:
>>>
>>> phenix.elbow generate_easy_r4.pdb --do-all 
>>>
>>>
>>>  -----------------------------------------------------------------
>>>       
>> -------------
>>     
>>>   electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3
>>>     - Nigel W. Moriarty (NWMoriarty at LBL.Gov)
>>>  -----------------------------------------------------------------
>>>       
>> -------------
>>     
>>>  Random number seed:  664322001
>>>  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
>>>  
>>> Can anyone suggests at this point, what I should do?
>>> Thanking you in advance...
>>>
>>> Raja 
>>>
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>>>   
>>>       
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