Patrick,
Zinc ions should be identified as ZN+2 at the end of the line for Refmac
(see modified line below):
12345678901234567890123456789012345678901234567890123456789012345678901234567890
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
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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.
>
> 12345678901234567890123456789012345678901234567890123456789012345678901234567890
> 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
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>
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