[phenixbb] creating cif for Zn
Raja Dey
rdey at usc.edu
Tue May 26 13:52:20 PDT 2009
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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