Hello all, I am trying to build a protein-ligand model using align-ligand.ali file. . Below is  the python script to generate 5 model and to  calculate the Dope and GA score. but I am unable to calculate the DOPE score and GA score. Plz help

from modeller import * from modeller.automodel import *

log.verbose()    # request verbose output env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']

env = environ() a = automodel(env, alnfile='alignment.ali',               knowns='5fd1', sequence='1fdx',               assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make()

Regards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand

________________________________ From: "modeller_usage-request@salilab.org" modeller_usage-request@salilab.org To: modeller_usage@salilab.org Sent: Tuesday, 10 April 2012 8:58 AM Subject: modeller_usage Digest, Vol 11, Issue 43

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1. Re: In what are the initial structures different?       (Modeller Caretaker)   2. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala)   3. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala)

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Message: 1 Date: Mon, 09 Apr 2012 11:46:02 -0700 From: Modeller Caretaker modeller-care@salilab.org To: BIN ZHANG zhngbn@gmail.com Cc: modeller_usage@salilab.org Subject: Re: [modeller_usage] In what are the initial structures     different? Message-ID: 4F832E6A.5020001@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 04/08/2012 11:58 PM, BIN ZHANG wrote: > I have a question about the differences of the initial structure built > for homology modeling. Can anyone tell me how exactly are these initial > structures different? Do they differ in the secondary structures in > uncertain regions? I cannot find this information in the manual.

See http://salilab.org/modeller/9.10/manual/node470.html, in particular step 3 and substep 3. The initial structures are simply randomized by calling selection.randomize_xyz().

Ben Webb, Modeller Caretaker