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
not
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.
Cheers,
Rob
--
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