"MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac."
1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali.
To obtain MODELLER visit : http://www.salilab.org/modeller/download_installation.html
Once MODELLER is installed edit patho_ePMV/extension/liste.txt to provide the pathtoModeller modlib library, e.g.:
Alternatively you can use the Add Extension in the extension menu from the gui.
Note : for windows users the MODELLER installation automatically
put the MODELLER library in the python Path. Thus MODELLER will be
automatically available in ePMV. We currently have tested XP and Vista.
Once modeller is available, a new menu item become available in the extension Window menu. This will open our simple MODELLER dialog. This dialog apply on the current molecule in ePMV. This dialog is active only if the use Modeller options was check before loading/browsing for a Molecule. (Edit->Option).
The dialog is decompose in 3 part :
Here is a simple demonstration in C4D: