Pat Loll wrote: > Thanks to all who replied. I wish I could give you a better explanation for why it didn't work in the earlier version.
See my posting, & various replies, a few days ago regarding "PDBSET bug with unusual (but legal) atom names" I think this (that is, Pat's) sort of annoyance will be increasingly frequent until the treatment of PDB files by the RCSB, REFMAC (program & libraries), and the rest of the CCP4 suite becomes uniform (which, gladly I can report, folks such as Garib, Eugene Krissinel, Francois Remacle, Kim Hendrick, and others ARE aware and are working to fix!). Dave > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Ian Tickle > Sent: Thursday, September 11, 2008 11:49 AM > To: [email protected] > Subject: Re: [ccp4bb] specifying metal ion names in PDB file > > 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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