Re: [ccp4bb]: Ion metals in pdb file

[Ethan Merritt <merritt@u.washington.edu>]

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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


-- 
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