Jack Shultz wrote: > I am new to modeller and I have not gone through the tutorial yet. I > have submitted a couple of FASTA format files to mod web. I am would > like to fix a problem with my docking complexes I get from autodock. > Some of them are missing atoms in a given residue. It was suggested I > either use Deep-View or Modeller to insert missing atoms. Can modeller > indeed achieve this? Are there any existing scripts to perform this?
Certainly - that is straightforward, and in fact Modeller will do it automatically. Just build a homology model using your existing model as a template (the alignment will be simply 1:1 since the sequences are the same). Use the regular modeling script at http://salilab.org/modeller/9v6/manual/node16.html
If you want to keep the original conformation of part of the system, use the script at http://salilab.org/modeller/9v6/manual/node23.html instead.
You can also use the same technique to fill in entire missing *residues*; see http://salilab.org/modeller/wiki/Missing%20residues for an example.
Ben Webb, Modeller Caretaker