In my case, the substrate is cellotetraose (4 glucose units). Should one
or four dots (....) to be added at the end of the alignment?
Each one-letter code in your alignment corresponds to one residue, so if
each glucose unit in your PDB has a different residue number, that's
four dots. If they're all in one PDB residue, one dot.
My other question in how do you build the alignment file (ali)? Do you
simply add the dots to the alignment file or is there any tricks?
Simply add the dots to your alignment. Residues in the alignment file
are listed in the same order as in the PDB.
wondering do we need to modify the PDB file to include the BLK or
HETATOM, and then create the ali?)
There should be no need to modify your PDB file.
When I tried to simply add the dots to the ali file and ran the script
to build the model, I got error with the structures not being recognized
and it complained about the sequence length.
You have to turn on env.io.hetatm first, otherwise Modeller will only
read the regular amino acids (ATOM records). See the examples in the
manual and tutorials.