{"action":"created","issue":{"url":"https://api.github.com/repos/pandegroup/openmm/issues/1072","labels_url":"https://api.github.com/repos/pandegroup/openmm/issues/1072/labels{/name}","comments_url":"https://api.github.com/repos/pandegroup/openmm/issues/1072/comments","events_url":"https://api.github.com/repos/pandegroup/openmm/issues/1072/events","html_url":"https://github.com/pandegroup/openmm/issues/1072","id":99055321,"number":1072,"title":"\"Fixed width overflow detected\" in PDBFile.writeFile with keepIds=True","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-08-04T20:30:07Z","updated_at":"2015-08-04T22:18:22Z","closed_at":null,"body":"We're trying to preserve original residue numberings in models generated by `simtk.openmm.app.Modeller` from constructs that match standard Uniprot numberings, but contain lots of solvent molecules. \r\n\r\nWriting out PDB files after the `Modeller` stage using \r\n```python2.7\r\n        app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile, keepIds=True)  \r\n```\r\ngives the error\r\n```\r\nFixed width overflow detected\r\n```\r\npresumably because too many waters are included.\r\n\r\nComplete input files here:\r\nhttps://gist.github.com/jchodera/d4e967c29fb124d76d44\r\n\r\nExample invocation (requires `pdbfixer-dev`):\r\n```\r\npython setup_mutations_ensembler.py --source_pdbfile='MTOR_HUMAN_D0-selected.pdb' --output_directory='MTOR_HUMAN_D0-mutations'\r\n```\r\n\r\nIs there some way we could have `writeFile` preserve numbering for non-water residues but do *something* to just not die on writing water residues (where we essentially *never* care about numbering being preserved)?"},"comment":{"url":"https://api.github.com/repos/pandegroup/openmm/issues/comments/127778082","html_url":"https://github.com/pandegroup/openmm/issues/1072#issuecomment-127778082","issue_url":"https://api.github.com/repos/pandegroup/openmm/issues/1072","id":127778082,"user":{"login":"peastman","id":4379786,"avatar_url":"https://avatars.githubusercontent.com/u/4379786?v=3","gravatar_id":"","url":"https://api.github.com/users/peastman","html_url":"https://github.com/peastman","followers_url":"https://api.github.com/users/peastman/followers","following_url":"https://api.github.com/users/peastman/following{/other_user}","gists_url":"https://api.github.com/users/peastman/gists{/gist_id}","starred_url":"https://api.github.com/users/peastman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/peastman/subscriptions","organizations_url":"https://api.github.com/users/peastman/orgs","repos_url":"https://api.github.com/users/peastman/repos","events_url":"https://api.github.com/users/peastman/events{/privacy}","received_events_url":"https://api.github.com/users/peastman/received_events","type":"User","site_admin":false},"created_at":"2015-08-04T22:18:22Z","updated_at":"2015-08-04T22:18:22Z","body":"How do you generate PDBx files?  Do you use the library from RCSB, or just write it out yourself?  We currently use their library for reading files, but I haven't looked at their API for writing to see whether it's flexible enough.  For example, can it write a series of frames that are generated one at a time by a simulation?"}}