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PDBeurope / arpeggio

Calculation of interatomic interactions in molecular structures
http://biosig.unimelb.edu.au/arpeggioweb/
GNU General Public License v3.0
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arpeggio not working at all #13

Open shoumo2021 opened 2 years ago

shoumo2021 commented 2 years ago

Hello - just cannot get arpeggio to work, and would much appreciate some help! Thanks Shoumo Installation as follows: conda create -n arpeggio-env python=3.7 anaconda conda activate arpeggio-env

In the arpeggio environment: conda install -c openbabel openbabel pip install git+https://github.com/PDBeurope/arpeggio.git@master#egg=arpeggio

openbabel 2.4.1 Python 3.7.13

(arpeggio-env) shoumo@Shoumos-MacBook-Pro pdb % arpeggio 1esr.pdb INFO//10:24:54.943//Program begin. WARNING//10:24:54.943//No selection was perceived. Defaults into full structure!! DEBUG//10:24:54.956//Loaded PDB structure (BioPython) DEBUG//10:24:55.523//Loaded PDB structure (OpenBabel) ERROR//10:24:55.524//An OpenBabel atom could not be matched to a BioPython counterpart. Traceback (most recent call last): File "/Users/shoumo/opt/anaconda3/envs/arpeggio-env/lib/python3.7/site-packages/arpeggio/core/interactions.py", line 1995, in _establish_structure_mappping biopython_atom = serial_to_bio[serial] KeyError: 0

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/Users/shoumo/opt/anaconda3/envs/arpeggio-env/bin/arpeggio", line 8, in sys.exit(main()) File "/Users/shoumo/opt/anaconda3/envs/arpeggio-env/lib/python3.7/site-packages/arpeggio/scripts/process_protein_cli.py", line 79, in main run_arpeggio(args) File "/Users/shoumo/opt/anaconda3/envs/arpeggio-env/lib/python3.7/site-packages/arpeggio/scripts/process_protein_cli.py", line 89, in run_arpeggio i_complex = InteractionComplex(args.filename, args.vdw_comp, args.interacting, args.ph) File "/Users/shoumo/opt/anaconda3/envs/arpeggio-env/lib/python3.7/site-packages/arpeggio/core/interactions.py", line 92, in init self._establish_structure_mappping() File "/Users/shoumo/opt/anaconda3/envs/arpeggio-env/lib/python3.7/site-packages/arpeggio/core/interactions.py", line 1998, in _establish_structure_mappping raise OBBioMatchError(serial) arpeggio.core.exceptions.OBBioMatchError: 0

roshkjr commented 1 year ago

arpeggio supports only structures in mmCIF format. PDB format is not supported