d'Auvergne protocol script mode - execution

Once the data is set up and you have modified your script to match your analysis needs, then the data pipe, pipe bundle and analysis variables are passed into the dAuvergne_protocol class. This is the final line of the script:

# Execution.

# Do not change!
dAuvergne_protocol(pipe_name=name, pipe_bundle=pipe_bundle, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, conv_loop=CONV_LOOP)

This script needs to be executed multiple times, once for each of the diffusion models. For example if the DIFF_MODEL variable is set to `ellipsoid', you can run relax with:

$ relax -tee log.ellipsoid dauvergne_protocol.py

You should use a different log file for each diffusion model, though relax will prevent you from overwriting an old log file. Note that the log.* files for each diffusion model may end up being a few gigabytes in size.

For a full analysis of a protein system, the analysis may require between one to two weeks to complete. This can be speed up using Gary Thompson's multi-processor code (see section 1.3 on page [*]). The analysis is performed as described in the previous sections and summarised in Figure 7.3. If you are curious, the implementation is within a very large relax script called auto_analyses/dauvergne_protocol.py (which must never be changed). This automatic analysis script hides all of the complexity of the full protocol from the sample script.

The relax user manual (PDF), created 2016-10-28.