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
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]
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
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
