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: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Roger Rowlett > Sent: 11 September 2008 16:24 > To: Ian Tickle > Cc: Patrick Loll; [email protected] > 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: [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]> > >>> > >>> > >> > > > > > > Disclaimer > > This communication is confidential and may contain > privileged information intended solely for the named > addressee(s). It may not be used or disclosed except for the > purpose for which it has been sent. 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