I have been using Modeller a few times for simple approaches but,
currently, I have to face a more complex problem. I have the crystal
structure of my template (740 residues, PDB: 4J0M) and I want to model
three putative homolog sequences coming from a different organism. In that
sense, the putative protein sequences are 1100 residues long, so I can
only model the region that it locally matches with my template. For this
reason, I have to use a local alignment (Smith-Waterman algorithm) between
the target and the template and you may imagine which kind of problems I
have to face when trying to run Modeller with this alignment: as it is a
local alignment, there are multiple positions in the pdb file that have
been skipped in the alignment so I have to remove those atoms from the pdb
file one by one. Additionally, there are missing positions in the crystal
template so I have to remake the alignment (deleting from the template
fasta file these residues) each time I find missing atoms in the pdb, plus
removing the atoms in the pdb file that do not match with the local
I am pretty sure there is a more intelligent and practical solution to this
problem since I have to do this for more than 700 residues and it can take
hours for only one model.
Since I am a new Modeller user and I have only used it for simple purposes,
any help you can provide it would be very appreciated.
Thank you very much for your attention and sorry for the inconvenience.