Re: [modeller_usage] missing sc atoms and rotamers
To: micheal j twin <>,
Subject: Re: [modeller_usage] missing sc atoms and rotamers
From: Modeller Caretaker <>
Date: Thu, 24 Oct 2013 17:03:26 -0700
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.