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SBGrid

SBGrid offers a comprehensive package of scientific software that is regularly updated and available on the cluster. It includes both module files and SBGrid's proprietary software loading utility. Currently, the suite comprises 543 applications, with multiple versions of each to accommodate the diverse needs of users. The SBGrid Consortium, which operates out of Harvard Medical School, is a research computing group funded by member research laboratories. It provides essential computing support to the global structural biology community.

Note: SBGrid users MUST be registered with the SBGrid Consortium to use this software package.

  1. To sign up for SBGrid access, simply go to the SBGrid Registration Page.
  2. Take note of the SBGrid License Agreement.
  3. Fill out the registration form.
  4. Take a screenshot of your completed registration acknowledgement.
  5. Send the screenshot to rtis.solutions.team@otago.ac.nz.
  6. This process must be done for each lab.

SBGrid Information WIKI

SBGrid on the Research Cluster

Modules

To use SBGrid via modules, use the following command export MODULEPATH=/programs/share/modulefiles/x86_64-linux:"$MODULEPATH"

Note

To make this permanent, add the above command to your .bashrc

Module Examples: Once the modulepath is loaded as above module avail will list all modules including SBGrid, Spack, and RTIS custom modules

module spider alphafold will search for all module packages include the SBGrid packages

Terminal

module spider alphafold

sbgrid/alphafold:
 Versions:
    sbgrid/alphafold/2.1.2
    sbgrid/alphafold/2.2.0
    sbgrid/alphafold/2.2.2
    sbgrid/alphafold/2.2.3
    sbgrid/alphafold/2.2.4
    sbgrid/alphafold/2.3.0
    sbgrid/alphafold/2.3.1
    sbgrid/alphafold/2.3.2_20241024
    sbgrid/alphafold/2.3.2
    sbgrid/alphafold/3.0.0_20241202_aa724ca
    sbgrid/alphafold/3.0.0

To load the SBGrid software simply type module load sbgrid/alphafold. This will load the default version of the software.

To load a specific version use module load sbgrid/alphafold/2.1.2

To show which versions are loaded module list

SBgrid Tools

To use SBGrid Tools, execute the following command source /programs/sbgrid.shrc

Note

To make this permanent, add the above command to your .bashrc

To load SBGrid software using the SBGrid tools instead of modules see SBGrid Getting Started

source /programs/sbgrid.shrc

Once you are in the SBGrid environment you can use all SBGrid commands.

https://sbgrid.org/wiki/examples

SBGrid youtube