Re: [modeller_usage] Filling in Missing atoms for a docking complex

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
-- 
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage