Looks like it's covalent in some compound 'DRG' so I guess the true
electron density will be somewhere intermediate between Cl and Cl-
depending on the relative electronegativity of the atom it's bonded to,
so take your pick as to which you think is closer. But yes, fully
ionised Cl should be 'Cl-1' and is listed in atomsf.lib as such.
-- Ian
> -----Original Message-----
> From: [log in to unmask]
> [mailto:[log in to unmask]] On Behalf Of Roger Rowlett
> Sent: 11 September 2008 16:24
> To: Ian Tickle
> Cc: Patrick Loll; [log in to unmask]
> Subject: Re: [ccp4bb] specifying metal ion names in PDB file
>
> 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.:
> >
> >
> 12345678901234567890123456789012345678901234567890123456789012
> 3456789012
> > 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: [log in to unmask]
> >> [mailto:[log in to unmask]] On Behalf Of Roger Rowlett
> >> Sent: 11 September 2008 14:37
> >> To: Patrick Loll
> >> Cc: [log in to unmask]
> >> 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: [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.
> >>>
> >>>
> >>>
> >> 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
> >>> [log in to unmask] <mailto:[log in to unmask]>
> >>>
> >>>
> >>
> >
> >
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