[phenixbb] creating cif for Zn
Raja Dey
rdey at usc.edu
Tue May 26 16:00:08 PDT 2009
Hi Pavel,
Thanks for your mail. Sorry, It was my mistake. I fixed that.
By the by, one more question.
I want to create Fo(native protein)-Fo(native protein + drug) map in phenix using the phase calculated from the refined structure of native protein to see if the density for the drug can pop up. Can you tell me how I can do that? I am now using version phenix-1.4-3. Do I need to install current version?
Thanks...
Raja
----- Original Message -----
From: Pavel Afonine <PAfonine at lbl.gov>
Date: Tuesday, May 26, 2009 1:58 pm
Subject: Re: [phenixbb] creating cif for Zn
To: PHENIX user mailing list <phenixbb at phenix-online.org>
> 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
> >>>
> >>> _______________________________________________
> >>> phenixbb mailing list
> >>> phenixbb at phenix-online.org
> >>> http://www.phenix-online.org/mailman/listinfo/phenixbb
> >>>
> >>>
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