Dear Ramana,
There is a script optimize.py. But MD+SA is already working. You won't get contrasting significant better model decoy. Run MODELLER for longer run to select decoy as per 3D-Jury or any other clustering method.
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
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To: "modeller usage" <>
Sent: Wednesday, April 20, 2011 2:50:13 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 73
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Today's Topics:
1. Re: Long loop modeling (bharat lal)
2. restrict salign to subparts of some structures sequences
(Benjamin SCHWARZ)
3. How to run flexEM package parallel ()
4. (no subject) ()
----------------------------------------------------------------------
Message: 1
Date: Fri, 15 Apr 2011 19:06:26 +0530 (IST)
From: bharat lal <>
Subject: Re: [modeller_usage] Long loop modeling
To: modeller <>
Message-ID: <>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I want ?to know whether long loop modeling of 30 or 40 residue length is possible through modeller or not ??..
----------?
Bharat
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Message: 2
Date: Mon, 18 Apr 2011 11:14:03 +0200
From: Benjamin SCHWARZ <>
Subject: [modeller_usage] restrict salign to subparts of some
structures sequences
To: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=us-ascii
Hello modellers,
I have a very large dataset of (beta propeller domain) structures, which I inspected visually to assess parts that sounded obviously not relevant for a structural alignment. For some structures I spotted long loops or several small helices insertions which I would like salign not to consider during the structural alignment. Is there a way to do so ?
thanks
--Ben.S
------------------------------
Message: 3
Date: Tue, 19 Apr 2011 14:55:04 -0700
From:
Subject: [modeller_usage] How to run flexEM package parallel
To:
Message-ID:
<>
Content-Type: text/plain;charset=utf-8
Hi, Ben,
I am using the flexEM package in modeller to refine a large complex.
However, it took a long time for one CG/MD cycle.
I wonder can I run the job in parallel ?
Maybe you can directly edit the script below.
Thanks!
Rui
#
============================================================================
#
# a. Define the type of oprimization: conjugate gradients minimization (CG)
# or molecular dynamics (MD)
# b. Edit input parameters: density map parameters and probe structure
#
# ======================= Maya Topf, 4 Dec 2007
=============================
from modeller import *
import shutil
import sys, os, os.path
import string
import math
from CG import opt_cg
from MD import opt_md
env = environ()
############### INPUT PARAMETERS ##################
optimization = 'MD' # type of optimization: CG / MD
rigid_filename = 'rigid.txt' # rigid bodies file name
path = './' # directory path
code = '1ake' # 4 letter code of the structure
input_pdb_file = '1ake_init.pdb' # input model for optimization
em_map_file = '1ake_10A.mrc' # name of EM density map (mrc)
format='MRC' # map format: MRC or XPLOR
apix=1.0 # voxel size: A/pixel
box_size=69 # size of the density map (cubic)
resolution=10.0 # resolution
x=-9.0; y=14.0; z=-8.0 # origin of the map
num_of_runs = 1 # number of runs
initial_dir = 1
############### RUN OPTIMIZATION ##################
# CG
# ----
if optimization == 'CG':
for i in range(initial_dir,initial_dir+num_of_runs):
scratch = path + '/' + str(i) + '/'
os.system("mkdir -p " + scratch)
os.system("cp " + path + '/'+ input_pdb_file + " " + scratch)
os.chdir(scratch)
opt_cg(path, code, str(i), 55*i, em_map_file, input_pdb_file,
format, apix, box_size, resolution, x, y, z, rigid_filename)
# MD
# ----
elif optimization == 'MD':
for i in range(initial_dir,initial_dir+num_of_runs):
scratch = path + '/' + str(i) + '/'
# input_pdb_file = 'final' + str(i) + '_cg.pdb'
# os.chdir(scratch)
opt_md(path, code, str(i), 10*i, em_map_file, input_pdb_file,
format, apix, box_size, resolution, x, y, z, rigid_filename)
------------------------------
Message: 4
Date: Wed, 20 Apr 2011 14:23:31 +0530 (IST)
From:
Subject: [modeller_usage] (no subject)
To:
Message-ID: <>
Content-Type: text/plain; charset="utf-8"
I have developed my homology models. wish to know how can I perform energy minimisation in Modeller?
Dr. Jayashree Ramana
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