On 10/23/13 8:15 AM, micheal j twin wrote: > I have 2 pdb structures of the same protein but with two different ligands. > The first pdb is complete while in the second structure some sidechains > atoms are missing. > What I need is to simply complete the missing sidechains in the second > pdb on the basis of the rotamers they have in the first structure.

You should be do this with Modeller, although it's not really designed for it:

1. Use complete_pdb() to make a complete structure for the second PDB (just with "wrong" sidechains).

2. Make an alignment using the two PDB structures as templates (presumably this a simple 1:1:1 100% identical alignment). Use the output structure from step 1 as the initial model.

3. Override automodel's select_atoms() to select only the missing sidechains, and then build comparative models as per usual. Those sidechains should inherit the dihedral preferences from the first PDB.

Ben Webb, Modeller Caretaker