[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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>>> phenixbb at phenix-online.org
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>>>
>>>
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