Re: [modeller_usage] How to incorporate NAD and water in my model
To: deepti <>
Subject: Re: [modeller_usage] How to incorporate NAD and water in my model
From: Modeller Caretaker <>
Date: Wed, 14 Mar 2007 09:17:04 -0700
Cc:
deepti wrote:
I am trying to construct a model for a protein having a known
structure for the purpose of learning Modeller.
The pdb structureis in form of protein-NAD adduct. My aim is to build a
similar model.
Using the templates I have built a model, please tell me how to
incorporate NAD and water in my model. I have read the manual 'faq' ,
but am confused how to change my alignment (including '.' for BLK
residues and 'w' ). How do I change the template pdb files for this?
How do I make my own restraint file?
There is no need to change your PDB file, or define custom restraints.
You simply tell Modeller to read in the HETATM and water residues from
the PDB (env.io.hetatm = True and env.io.water = True) and then list all
of those residues in your template sequence in your alignment (. for
HETATM, w for water). You can then use the target sequence alignment as
per usual to list the residues you want to appear in your final model
(generally people use a 1:1 alignment for the . and w residues).