{"action":"opened","issue":{"url":"https://api.github.com/repos/rigdenlab/ample/issues/58","repository_url":"https://api.github.com/repos/rigdenlab/ample","labels_url":"https://api.github.com/repos/rigdenlab/ample/issues/58/labels{/name}","comments_url":"https://api.github.com/repos/rigdenlab/ample/issues/58/comments","events_url":"https://api.github.com/repos/rigdenlab/ample/issues/58/events","html_url":"https://github.com/rigdenlab/ample/issues/58","id":353284103,"node_id":"MDU6SXNzdWUzNTMyODQxMDM=","number":58,"title":"Check that the fasta sequence and residues in the benchmark pdb match","user":{"login":"linucks","id":9549700,"node_id":"MDQ6VXNlcjk1NDk3MDA=","avatar_url":"https://avatars3.githubusercontent.com/u/9549700?v=4","gravatar_id":"","url":"https://api.github.com/users/linucks","html_url":"https://github.com/linucks","followers_url":"https://api.github.com/users/linucks/followers","following_url":"https://api.github.com/users/linucks/following{/other_user}","gists_url":"https://api.github.com/users/linucks/gists{/gist_id}","starred_url":"https://api.github.com/users/linucks/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/linucks/subscriptions","organizations_url":"https://api.github.com/users/linucks/orgs","repos_url":"https://api.github.com/users/linucks/repos","events_url":"https://api.github.com/users/linucks/events{/privacy}","received_events_url":"https://api.github.com/users/linucks/received_events","type":"User","site_admin":false},"labels":[{"id":562987815,"node_id":"MDU6TGFiZWw1NjI5ODc4MTU=","url":"https://api.github.com/repos/rigdenlab/ample/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-23T08:50:20Z","updated_at":"2018-08-23T08:50:20Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"If the sequence given to ROSETTA to model and that in the native pdb file (supplied with the -native_pdb flag) don't match, then the benchmarking will crash with:\r\n\r\nINFO: Using single structure provided for all model comparisons\r\nINFO: Direct comparison of models and structures\r\n----------------------------EICV-TA\r\nTSSVLRSPMPGVVVAVSVKPGDAVAEGQEICVIEA\r\nTraceback (most recent call last):\r\n  File \"/home/jmht/ccp4-7.0/lib/python2.7/runpy.py\", line 162, in _run_module_as_main\r\n    \"__main__\", fname, loader, pkg_name)\r\n  File \"/home/jmht/ccp4-7.0/lib/python2.7/runpy.py\", line 72, in _run_code\r\n    exec code in run_globals\r\n  File \"/home/jmht/ample.git/ample/util/tm_util.py\", line 658, in <module>\r\n    main()\r\n  File \"/home/jmht/ample.git/ample/util/tm_util.py\", line 642, in main\r\n    tmapp.compare_structures(args.models, args.structures, fastas=args.fastas, all_vs_all=args.allvall)\r\n  File \"/home/jmht/ample.git/ample/util/tm_util.py\", line 437, in compare_structures\r\n    pdb_combo = self._mod_structures(model_aln, structure_aln, model, structure)\r\n  File \"/home/jmht/ample.git/ample/util/tm_util.py\", line 510, in _mod_structures\r\n    raise RuntimeError(msg % (model_name, structure_name))\r\nRuntimeError: Differing residues in model and structure. Affected PDBs S_00000012_10_0dqz6csdh8_mod - 2JKU_std_std\r\n\r\nWe should check that the sequence and residues in the PDB file match at the start"}}
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