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LPDI-EPFL / masif_seed

Masif seed paper repository
Apache License 2.0
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Error when running extract_helix_one #1

Closed ShuhaoGithub closed 1 year ago

ShuhaoGithub commented 1 year ago

Hi, I ran into this error when running the first step of masif_seed. May I ask how to solve this? Thanks!

root@df6a6de34df2:/masif/design/masif_seed/masif/data/masif_peptides# ./data_extract_helix_one.sh 4QVF_B Downloading PDB structure '4QVF'... Protonating file /var/tmp/4QVF.pdb Traceback (most recent call last): File "/masif/design/masif_seed/masif/source/data_preparation/01b-helix_extract_and_triangulate.py", line 75, in helices = computeHelices(pdb_id, pdb_filename, chain_id) File "/masif/design/masif_seed/masif/source/data_preparation/01b-helix_extract_and_triangulate.py", line 33, in computeHelices dssp = DSSP(model, pdbfilename) File "/usr/local/lib/python3.6/site-packages/Bio/PDB/DSSP.py", line 438, in init dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp) File "/usr/local/lib/python3.6/site-packages/Bio/PDB/DSSP.py", line 236, in dssp_dict_from_pdb_file stderr=subprocess.PIPE, File "/usr/local/lib/python3.6/subprocess.py", line 709, in init restore_signals, start_new_session) File "/usr/local/lib/python3.6/subprocess.py", line 1344, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'mkdssp': 'mkdssp'

bud-graziano commented 1 year ago

Hi Shuhao, unfortunately I wasn't able to reproduce the error...

Just to double-check, you're running MaSIF within the docker container, correct?

Could you please provide the output of apt list --installed and pip3 list?

ShuhaoGithub commented 1 year ago

Hi Andreas, thank you for the reply! Yes I used the container. I was able to successfully ran it on a different machine so it's good now. Thank you!