EasyModeller4 Manual
EasyModeller4 Manual
Previous Versions
EasyModeller 1.0 : A basic Windows based GUI to modeller with simple features
EasyModeller 2.0 : A windows based GUI with robust error handling and a much user friendly GUI
EasyModeller 2.1 : EasyModeller 2.0 with BioEdit support for Alignment Editing
EasyModeller 3.0 : A LINUX based GUI to Modeller introducing on the fly code editing
Publication Link : EasyModeller: A graphical interface to MODELLER
EasyModeller 4.0
EasyModeller 4.0 introduces a fresh new GUI for Homology Modeling using MODELLER in the
backend and available for both Windows and Linux platform. This version has several new features
integrating all the goodies of EasyModeller 3.0 which was only available for LINUX.
Installation
Windows :
EasyModeller requires the following softwares to be installed in your system to run
1. Modeller (Freely available at salilab.org)
2. Compatible Python version (Freely available at www.python.org)
For older versions of Modeller use Python 2.5 or 2.6
For latest Modeller use Python 2.7
Python 3.x is not supported by EasyModeller
N.B:
1. If you have Python installed and was still asked with a popup box stating "Windows cannot find
a software for test.py" then probably you have not associated the .py files to Python
2. Make sure that you have installed Modeller in the default location i.e, C:\\Program Files
3. Windows7 / Vista users may need to run the application by Right clicking on the application
and select "Run as Administrator"
If you still face any errors you can always mail me at [email protected]
Linux
For this version of EasyModeller there are the following simple requisites :
1. A Linux operating system ( Fedora, Ubuntu, etc.)
2. Python : Will be installed by default in all Linux systems.
3. Modeller : To be installed (preferably the latest version ).
4. Rasmol / Pymol / Jmol : Any of the three PDB viewer should be in the path.
Download the appropriate Modeller from here ( For Fedora and other Red Hat based Linux :
Linux (32-bit RPM) and For Ubuntu and other Debian based OS : Linux
(http://salilab.org/modeller/9.10/modeller_9.10-1_i386.deb) .
Obtain the Modeller key from Here
Installation for Linux (RPM) : Fedora
Install the RPM file by running the following command (either logging in as the root user, or by
prepending the command with 'sudo'), replacing XXXX with the Modeller license key (and i386
with ia64 or x86_64 if necessary).
env KEY_MODELLER=XXXX rpm -Uvh modeller-9.10-1.i386.rpm
Installation for Linux (Debian) : Ubuntu
Install the package by running the following command, replacing XXXX with the Modeller license
key (and i386 with x86_64 if you are using the 64-bit installer).
sudo env KEY_MODELLER=XXXX dpkg -i modeller_9.10-1_i386.deb
The code for the alignment can be seen by using the button Edit Code. This will display a new
window with the corresponding code which can be edited on the fly and the Run feature can be
used to run the edited code. The generated alignment can be zoomed in and out and can also be
saved as a postscript image file. The Edit Alignement feature can be used to edit the generated
alignment.
The generated models appear in the box Generated Models and can be manipulated using a suite
of features. The DOPE profile viewer can be used to generate a DOPE profile plot of the generated
models or a superimposed plot of the generated model with the template which can be chosen
from a popup box that would allow to choose the structures for generating the plot. The generated
plot can be zoomed using mouse selection.
A Ramachandran plot can be generated for a model selected in the box. The plot can be zoomed
using mouse selection and mouse over on a dot indicates its residue number and name. The red
boundary forms the core region and the blue boundary forms the allowed region of the plot. A
good model should have more than 90% residues in the allowed region.
The Loop model feature can be used to model a loop in the model by selecting the starting and
ending residue of the loop. The generated models can also be optimized using the Optimize
feature which allows the user to perform simple conjugate gradient and steepest descent based
molecular optimization of the model. A simple molecular dynamics feature is also implemented for
performing basic dynamics study on the models. The View Model feature can be used to view the
3d structure of the generated models using the default PDB viewer installed in the system.
Structural and mechanistic determinants of a novel site for noncompetitive inhibition of GluN2Dcontaining NMDA receptors.
Hansen KB, Traynelis SF.
J Neurosci. 2011 Mar 9;31(10):3650-61.
PMID:21389220
Phosphorylation Alters the Interaction of the Arabidopsis Phosphotransfer Protein AHP1 with Its Sensor
Kinase ETR1
Scharein B, Groth G
PLoS ONE , 2011,6(9): e24173.
doi:10.1371/journal.pone.0024173
The NMR structure of stomagen reveals the basis of stomatal density regulation by plant peptide
hormones.
Ohki S, Takeuchi M, Mori M.
Nat Commun. 2011 Oct 25;2:512. doi: 10.1038/ncomms1520.