[ccp4bb] specifying metal ion names in PDB file

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: postdoctoral position at the Salk Institute
From: Witek Kwiatkowski witek {- at -} PERUTZ {- dot -} SALK {- dot -} EDU
Date: 2008-09-11

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Subject: Re: specifying metal ion names in PDB file
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2008-09-11

Subject: specifying metal ion names in PDB file
From: Patrick Loll pat {- dot -} loll {- at -} DREXEL {- dot -} EDU
Date: 2008-09-11

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.

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

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
pat.loll@drexelmed.edu

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: postdoctoral position at the Salk Institute
From: Witek Kwiatkowski witek {- at -} PERUTZ {- dot -} SALK {- dot -} EDU
Date: 2008-09-11

Next message:
Subject: Re: specifying metal ion names in PDB file
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2008-09-11