Oops, yes. Element symbol right-justified in 77-78, charge in 79-80. Out
of curiosity, shouldn't "CL " technically be listed as "CL-1" in the
PDB file for Refmac as well?
Cheers,
Roger Rowlett
Ian Tickle wrote:
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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Roger Rowlett
Sent: 11 September 2008 14:37
To: Patrick Loll
Cc: [email protected]
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: [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.
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
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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