In the Sali Lab

If you are working in the Sali lab, you don’t need to build and install AllosMod - it is already set up for you as a module. Just run module load allosmod to load it.


  • Python 2.6 or later (Python 3 should also be OK).
  • MODELLER. This library expects to be able to directly import the Modeller Python package (via import modeller) and to run the Modeller binary (e.g. mod9.15). If you installed Modeller from the .tar.gz package, you will need to set the PYTHONPATH, PATH and LD_LIBRARY_PATH environment variables to facilitate this.
  • DSSP. It is expected that the mkdssp binary is in the PATH.
  • nose is also needed to run the test suite (recommended but not essential).

If you will also be using SAXS profiles (e.g. for the AllosMod-FoXS web service) then you will need:

  • ProFit. The profit binary needs to be in the PATH.

In the Sali lab, running module load modeller dssp profit will get all of these dependencies.


Use make test to test the library, and make install to install it. In most cases you will need to tell make where to install (if running on a Linux cluster, AllosMod will need to be installed on a network-accessible filesystem) and where any temporary/scratch disks usable by AllosMod are. (AllosMod needs a ‘local’ scratch disk, accessible by individual jobs on each node, as well as a ‘global’ scratch disk, on a network-accessible filesystem.) Do this with something like make PREFIX=/shared/allosmod GLOBAL_SCRATCH=/scratch install. See Makefile.include for all make variables that can be configured.