Script to reproduce the modelling step in the best single template method in 
CAMEO [1] once you identified the required templates/ alignments using 
TMalign [2]

Requires a full ProMod3 installation with the pm executable in your path to run. 
If profiles need to be calculated, an HHblits installation (version 2.0.16) and 
an NR20 sequence database are also required.

print the help and exit:
pm CAMEO_bst.py -h

run without providing a sequence profile (not recommended):
pm CAMEO_bst.py test_tpl.pdb test_aln.fasta

run with precalculated sequence profile:
pm CAMEO_bst.py test_tpl.pdb test_aln.fasta -p test_profile.hhm

run with profile calculation:
pm CAMEO_bst.py test_tpl.pdb test_aln.fasta -r <PATH_TO_HHBLITS_INSTALLATION> -n <PATH_TO_NR_DATABASE>

[1] Haas et al., Introducing "best single template" models as reference baseline 
    for the Continuous Automated Model Evaluation (CAMEO), Proteins, 87: 1378–1387 (2019)
[2] Y. Zhang and J. Skolnick, TM-align: A protein structure alignment algorithm 
    based on TM-score, Nucleic Acids Research, 33: 2302-2309 (2005) 

