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Re: [modeller_usage] Heme

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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage