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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: [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. > > 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 > [log in to unmask] <mailto:[log in to unmask]> >