[phenixbb] creating cif for Zn

[Raja Dey]

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 
> >>>
> >>> _______________________________________________
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> >>> phenixbb at phenix-online.org
> >>> http://www.phenix-online.org/mailman/listinfo/phenixbb
> >>>   
> >>>       
> >> _______________________________________________
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> >>
> >>     
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>