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