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 ...

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. This web site presents a tutorial for the use of MODELLER 10.0 or newer (for older versions of MODELLER, use the old MODELLER 9v4 tutorial). There are 5 modeling examples that ...

MODELLER is available free of charge to academic non-profit institutions; you will, however, need to register for a license in order to use the software. It is also available through BIOVIA for government research labs and commercial entities. Modeller 10.6, released Oct. 22nd, 2024

2024年10月17日 · EnergyData.dynamic_modeller — calculate non-bonded spline restraints; EnergyData.excl_local — exclude certain local pairs of atoms; EnergyData.radii_factor — scale atomic radii; EnergyData.lennard_jones_switch — Lennard-Jones switching parameters; EnergyData.coulomb_switch — Coulomb switching parameters

For a step-by-step guide to building models with Modeller, with specific examples ranging from the basic to the difficult, try the Modeller tutorial. Documentation is also available for older releases of Modeller. Supplementary material is also available for several of our past workshops and publications, and is made available for completeness ...

Wishlist: features desired in future Modeller releases. Patches: hotfixes for problems with the current Modeller release. Old operating systems: workarounds for using Modeller on old systems. Packages: third-party-provided Modeller packages for some other operating systems. Modules: using Modeller with the module command.

For example, to run this script using Modeller 10.0's own interpreter, use mod10.0 build_profile.py. Note that mod10.0 automatically creates a build_profile.log logfile. (You can get a command line using xterm or GNOME Terminal in Linux, Terminal in Mac OS X, or the 'Modeller' link from your Start Menu in Windows.

To obtain a MODELLER license key (which you need to install and run MODELLER) please fill out the following License Agreement. Note that MODELLER is available free of charge only to academic non-profit institutions; for commercial entities or government research labs (such as the NIH and national labs in the USA), see the non-academic licensing ...

(See below for example scripts.) (Modeller itself can be found in the /Library/modeller-10.5/ directory.) Note that Modeller is only set up to work with the standard Apple-provided Python, i.e. /usr/bin/python or /usr/bin/python3; to make it work with other versions of Python installed on your system, you may need to modify PYTHONPATH. (In ...

Modeller execution under Windows from the command line Modeller does not have a graphical user interface but is a command line tool. You have to open a command prompt window and execute modeller with giving it an argument: Programs-Accessories-CommandPrompt gives you the command prompt window The Readme file states: 5.