Hi, it's not clear why this should be necessary in general since
$CLIBD/atomsf.lib contains entries for both Zn & Zn+2:
Zn
30 30 1.304100
14.074300 7.031800 5.162500 2.410000
3.265500 0.233300 10.316299 58.709702
-1.612000 0.678000 0.222000 1.431000
Zn+2
30 28 0.780700
11.971900 7.386200 6.466800 1.394000
2.994600 0.203100 7.082600 18.099499
-1.612000 0.678000 0.222000 1.431000
Nevertheless in this particular the ionised form is no doubt more
appropriate than the elemental one.
But anyway shouldn't the atomic symbols go in cols 77-80, not 72-75?
i.e.:
123456789012345678901234567890123456789012345678901234567890123456789012
34567890
ATOM 3048 CLBB DRG X 1 1.461 37.707 15.068 1.00 37.36
CL
ATOM 3155 O HOH H 318 -2.609 36.139 -25.338 1.00 48.47
O
HETATM 3156 ZN ZN A 981 4.451 8.580 3.686 1.00 31.06
ZN+2
Cheers
-- Ian
> -----Original Message-----
> From: [log in to unmask]
> [mailto:[log in to unmask]] On Behalf Of Roger Rowlett
> Sent: 11 September 2008 14:37
> To: Patrick Loll
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] specifying metal ion names in PDB file
>
> Patrick,
>
> Zinc ions should be identified as ZN+2 at the end of the line
> for Refmac
> (see modified line below):
>
> 12345678901234567890123456789012345678901234567890123456789012
> 345678901234567890
> ATOM 3048 CLBB DRG X 1 1.461 37.707 15.068 1.00
> 37.36 CL
> ATOM 3155 O HOH H 318 -2.609 36.139 -25.338 1.00
> 48.47 O
> HETATM 3156 ZN ZN A 981 4.451 8.580 3.686 1.00
> 31.06 ZN+2
>
> Cheers,
>
> --
> --------------------------------------------------------------
> ----------
> Roger S. Rowlett
> Professor
> Colgate University Presidential Scholar
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> tel: (315)-228-7245
> ofc: (315)-228-7395
> fax: (315)-228-7935
> email: [log in to unmask]
>
>
> Patrick Loll wrote:
> > Hi,
> >
> > I know this has been covered ad infinitum, yet we find ourselves
> > unable to get Refmac to recognize a zinc ion in the PDB file.
> >
> >
> 12345678901234567890123456789012345678901234567890123456789012
> 345678901234567890
> > ATOM 3048 CLBB DRG X 1 1.461 37.707 15.068
> 1.00 37.36 CL
> > ATOM 3155 O HOH H 318 -2.609 36.139 -25.338
> 1.00 48.47 O
> > HETATM 3156 ZN ZN A 981 4.451 8.580 3.686
> 1.00 31.06 ZN+2
> >
> > The chlorine in the above example is read properly, but the
> zinc is not:
> >
> > FORMATTED OLD file opened on unit 45
> > Logical name: ATOMSF,
> > Filename: /sw/share/xtal/ccp4-6.0.2/lib/data/atomsf.lib
> > No match for atom ID ZN subtracting one character
> > No match for atom ID Z giving up!
> >
> > Note that the register of the atom name appears correct.
> We've tried
> > a zillion permutations including using ATOM/HETATM, moving
> the residue
> > name so it's left-justified, playing with the position of the name
> > over in columns 70-72, using Zn instead of ZN,...
> >
> > Any words of wisdom? It's embarrassing to be hung up on
> something so
> > simple and obvious, yet hung up we are.
> >
> > Pat
> >
> >
> >
> --------------------------------------------------------------
> -------------------------
> > Patrick J. Loll, Ph. D.
> > Professor of Biochemistry & Molecular Biology
> > Director, Biochemistry Graduate Program
> > Drexel University College of Medicine
> > Room 10-102 New College Building
> > 245 N. 15th St., Mailstop 497
> > Philadelphia, PA 19102-1192 USA
> >
> > (215) 762-7706
> > [log in to unmask] <mailto:[log in to unmask]>
> >
>
>
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