Installation

To obtain ModelMaker using git, type the following command in a terminal:

SSH:

git clone git@github.com:ryanmcgreevy/ModelMaker.git    

HTTPS:

git clone https://github.com/ryanmcgreevy/ModelMaker.git  

or download the zip file and extract it.

To use ModelMaker, add the following to your ~/.vmdrc:

set env(ROSETTADB) "/your/path/to/rosetta/main/database"
set env(ROSETTAPATH) "/your/path/to/rosetta/main/source/bin"
set auto_path [linsert $auto_path 0 /your/path/to/modelmaker]
package require modelmaker

Make sure to replace the paths with the correct ones specific to the location of your Rosetta and ModelMaker folders.

You can also set the env(ROSETTAEXE) environment variable to use a specific set of Rosetta binaries. This environment variable should be set to the binary prefix you wish to use, but will be set by default depending on your platform. (e.g., on OSX, this environment variable will usually be static.macosclangrelease)

MPI

If you want to use the parallel MPI version of Rosetta, you must compile the MPI binaries with the following command:

./scons.py bin mode=release extras=mpi

For more information please see the Rosetta Documentation.

Then you will need to set your env(ROSETTAEXE) environment variable to the prefix of the MPI binaries (usually mpi.* where * is the rest of the specific platform, like macosclangrelease or linuxgccrelease) and set the -np option in the ModelMaker commands to specify the number of processors to use.

In VMD's TkConsole, type modelmaker to see a list of commands. You can also type modelmaker command where 'command' is one of the available ModelMaker commands to see more information about it.