[stability_pipeline] prism-to-mut mapping error when having pdb file with several chains
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j0kaso commented
wrong resdata_reverse counting if e.g. chain C should be used (starting with chain A for counting). error rises in prism-to-mut.
example call for testing:
python /groups/sbinlab/tiemann/repos/PRISM/PRISM/software/rosetta_ddG_pipeline/run_pipeline.py \
--structure /groups/sbinlab/tiemann/projects/PRISM/2020_09-parameter_tuning/input_final/OmpLA/1qd6.pdb \
--mutate_mode prism \
--prism /groups/sbinlab/tiemann/projects/PRISM/2020_09-parameter_tuning/input_final/OmpLA/prism_mave_102-106_OmpLA_ecoli.txt \
--outputpath /groups/sbinlab/tiemann/projects/PRISM/2020_09-parameter_tuning/output-benchmark_relax_test/OmpLA/relaxrep1_relaxstruc20_repeat5_repack8.0 \
--mode fullrun --chainid C --is_membrane True --mp_calc_span_mode DSSP --mp_align_ref 1qd6_C \
--mp_prep_align_mode OPM --benchmark_mp_repack 8.0 --benchmark_mp_repeat 5 --benchmark_mp_relax_repeat 1 \
--benchmark_mp_relax_strucs 1 --slurm_partition sbinlab --overwrite_path True
j0kaso commented
prism option not available anymore use mutfiles