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:[log in to unmask]] On
> Behalf Of Ian Tickle
> Sent: Thursday, September 11, 2008 11:49 AM
> To: [log in to unmask]
> 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: [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]>
> > >>>
> > >>>
> > >>
> > >
> > >
> > > 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. If you are not the
> > intended recipient you must not review, use, disclose, copy,
> > distribute or take any action in reliance upon it. If you
> > have received this communication in error, please notify
> > Astex Therapeutics Ltd by emailing
> > [log in to unmask] and destroy all copies of the
> > message and any attached documents.
> > > Astex Therapeutics Ltd monitors, controls and protects all
> > its messaging traffic in compliance with its corporate email
> > policy. The Company accepts no liability or responsibility
> > for any onward transmission or use of emails and attachments
> > having left the Astex Therapeutics domain. Unless expressly
> > stated, opinions in this message are those of the individual
> > sender and not of Astex Therapeutics Ltd. The recipient
> > should check this email and any attachments for the presence
> > of computer viruses. Astex Therapeutics Ltd accepts no
> > liability for damage caused by any virus transmitted by this
> > email. E-mail is susceptible to data corruption,
> > interception, unauthorized amendment, and tampering, Astex
> > Therapeutics Ltd only send and receive e-mails on the basis
> > that the Company is not liable for any such alteration or any
> > consequences thereof.
> > > Astex Therapeutics Ltd., Registered in England at 436
> > Cambridge Science Park, Cambridge CB4 0QA under number 3751674
> > >
> > >
> > >
> >
> >
>
>
> 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. If you are not the intended recipient you
> must not review, use, disclose, copy, distribute or take any
> action in reliance upon it. If you have received this
> communication in error, please notify Astex Therapeutics Ltd
> by emailing [log in to unmask] and destroy all
> copies of the message and any attached documents.
> Astex Therapeutics Ltd monitors, controls and protects all
> its messaging traffic in compliance with its corporate email
> policy. The Company accepts no liability or responsibility
> for any onward transmission or use of emails and attachments
> having left the Astex Therapeutics domain. Unless expressly
> stated, opinions in this message are those of the individual
> sender and not of Astex Therapeutics Ltd. The recipient
> should check this email and any attachments for the presence
> of computer viruses. Astex Therapeutics Ltd accepts no
> liability for damage caused by any virus transmitted by this
> email. E-mail is susceptible to data corruption,
> interception, unauthorized amendment, and tampering, Astex
> Therapeutics Ltd only send and receive e-mails on the basis
> that the Company is not liable for any such alteration or any
> consequences thereof.
> Astex Therapeutics Ltd., Registered in England at 436
> Cambridge Science Park, Cambridge CB4 0QA under number 3751674
>
|