I'm using lattest version of Modeller with the Easy Modeller GUI.
I'm modelling Green fluorescent protein (GFP) which consist of
chromophore heterogroup which is covalently lincked in the middle of
the sequence of that protein ( so this HET group is missing in the
fasta sequence of that protein- and during sequence-template alignment
I obtained GAP in the place where Chromophore group should be).
How I could model this protein with inclusion of the Heterogroup in
the final model ?
If the HETATM residue is present in your template, you can simply set
env.io.hetatm=True and add a BLK ('.') residue to the alignment in both
the template and the sequence. Modeller will just copy the HETATM
residue from the template to the model. There are examples of this in
the manual and tutorial.