[phenixbb] creating cif for Zn

[Raja Dey]

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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