IR asymmetric unit modelling

For modelling the IR asymmetric unit the local rigid body refinement method from Assembline will be used. The dir scnpc_tutorial/IR_asymmetric_unit_refinement includes source code files, input files and precalculated modelling results for the IR unit:

- parameters file & configuration file for 'refinement' integrative modelling of wt IR unit
- sequence fasta file, input_PDB, EM (input data)
- IR_unit_final_refined_model, out (output modelling results)

1. First activate your virtual environment and enter the IR_asymmetric_unit_refinement dir

   source activate Assembline
   
   cd IR_asymmetric_unit_refinement/
   

   or depending on your computer setup:

   conda activate Assembline
   
   cd IR_asymmetric_unit_refinement/
   

2. Run the refinement

   # this will run 500 refinement modelling runs on a slurm cluster (for options/parameters or local runs inspect the Assembline manual)
   assembline.py --traj --models -o out --multi --start_idx 0 --njobs 500 config.json params.py
   

   Note

   There is already an output dir IR_asymmetric_unit_refinement/out so in case you want to run the modelling then rename the out/ dir as it will be overwritten from the run above

3. Enter out/ dir, generate output scoring lists and rebuild atomic structures of models

   cd out
   
   extract_scores.py #this should create a couple of files including all_scores_sorted_uniq.csv
   
   rebuild_atomic.py --top 10 --project_dir <full path to the original project directory IR_asymmetric_unit_refinement> config.json all_scores_sorted_uniq.csv
   

4. While in the out/ dir run the following command to prepare your output models for analysis with imp-sampcon tool from IMP

   setup_analysis.py -s all_scores.csv -o analysis -d density.txt
   

   Note

   The density.txt is not provided therefore inspect an example file in CR_Y_complex/out. To generate it yourself please inspect Assembline analysis section.

5. Run imp-sampcon exhaust tool (command-line tool provided with IMP) to perform the sampling analysis:

   cd analysis
   
   imp_sampcon exhaust -n <prefix for output files> \
   --rmfA sample_A/sample_A_models.rmf3 \
   --rmfB sample_B/sample_B_models.rmf3 \
   --scoreA scoresA.txt --scoreB scoresB.txt \
   -d ../density.txt \
   -m cpu_omp \
   -c <int for cores to process> \
   -gp \
   -g <float with clustering threshold step> \
   

   Note

   For further descriptions of settings for imp_sampcon please see Sampling exhaustiveness and precision with Assembline