Bo Yang wrote:
> I have heme modeled into my target using Modeller. When I try to
> visualize the model, the Fe is not shown. I check the pdb file of the
> model, Fe is there. I couldn't understand what could be wrong. Why can't
> "Fe" be visuallized?
>
> I use Modeller 8v1. The program used for structure visuallization are
> Chimera and VMD.
You should use Modeller 9v5 - 8v1 is very old. Your visualization
problem seems likely to be one or both of the following problems, both
of which should no longer be present in 9v5:
1. Heme residue is written out as residue type 'BLK' rather than 'HEM'.
2. FE atom record is in the wrong column.
Problem (1) is no longer present in 9v5 - it preserves the original
residue names for '.' residues.
Problem (2) is most likely a problem with your input PDB template file
if it happens with Modeller 9v5, since the atom names are written out
exactly as in the input PDB.
Ben Webb, Modeller Caretaker
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