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Re: [modeller_usage] Heme

Hi Bo,

On Tue, 04 Nov 2008 03:04:10 -0800 (PST), Bo Yang <> wrote:

> I use dot (.) . Heme is shown as BLK in the model. Using Chimera and
> VMD, the whole molecule of heme is there, but not Fe. If I select "Fe"
> from "element", no selection returns. The "Fe" is in the pdb file as
> shown below:
> HETATM 3620  FE  BLK   455    
> -54.160  -1.094 -33.073 
> 1.00999.99       1SG3621

I think the problem is just that modeller is not writing out the atom name
correctly.  In a proper PDB file, the element symbol should be right-justified
in columns 13-14.  So your line above should start with:

HETATM 3620 FE   BLK   455
HETATM 3620  FE  BLK   455

If you edit the PDB files as output by modeller you can fix that.  Otherwise,
you need to select the Fe by atom name, rather than element in Chimera or VMD.
I have seen the same problem when incorporating calcium ions in a structure.

Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<>    http://pldserver1.biochem.queensu.ca/~rlc