Hi Bo,
On Tue, 04 Nov 2008 03:04:10 -0800 (PST), Bo Yang n62star@yahoo.com 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