[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ccp4bb]: Ion metals in pdb file
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Ethan Merritt wrote:
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> On Thursday 10 January 2002 12:13, Kiki Pavlou wrote:
> > Hi all,
> >
> > I am wondering if anyone could propose any solutions to my problem:
> > I am using Refmac 4.0 and I am trying unsuccessfully to insert ion metals
> > ( Calcium and Manganese) in my pdb file.
> > The input file looks as follows at this specific part:
> >
> > ATOM 2214 MN IUM B 240 29.813 11.768 45.332
> > 1.00 30.08 B ATOM 2215 CA IUM B 241
> > 26.948 11.566 48.495 1.00 20.07 B
> >
> > and in my protin input file as:
> >
> > VDWRADII 7 C 1 3.7 N 2 3.1 O 3 3.0 S 4 3.6 CA 7
> > 3.8 MN 8 3.8 OW0 10 3.0
> >
> > I am running the program and in the output pdb file the ions disappear.
>
> Amazingly enough, I just spent the morning sorting out precisely this problem.
> The answer is to make sure that your atom name appears *exactly* the same
> (case sensitive!) in
> 1) the PDB file
> 2) protin.dic (one of the IUM records)
> 3) $CLIB/data/atomsf.lib
>
> It's the atomsf.lib entry that actually determs the scattering type of the atom.
> Note that the default entries in protin.dic and atomsf.lib don't match;
> protin.dic has MN while atomsf.lib has Mn Mn+2 Mn+3 Mn+4 but not MN
>
But the case of the atom id is not important for atomsf.lib or at least
I didnt think so?
It is for matching to the dictionary, whether you e using PROTIN or
REMAC5
But in this case I suspect the metal id is in the wrong column..
Eleanor
> --
> Ethan A Merritt merritt@u.washington.edu
> Biomolecular Structure Center Box 357742
> University of Washington, Seattle, WA 98195
> phone: (206)543-1421
> FAX: (206)685-7002