{"action":"created","issue":{"url":"https://api.github.com/repos/Acellera/htmd/issues/76","repository_url":"https://api.github.com/repos/Acellera/htmd","labels_url":"https://api.github.com/repos/Acellera/htmd/issues/76/labels{/name}","comments_url":"https://api.github.com/repos/Acellera/htmd/issues/76/comments","events_url":"https://api.github.com/repos/Acellera/htmd/issues/76/events","html_url":"https://github.com/Acellera/htmd/issues/76","id":163059137,"number":76,"title":"proteinPrepare strange results","user":{"login":"giadefa","id":7776826,"avatar_url":"https://avatars.githubusercontent.com/u/7776826?v=3","gravatar_id":"","url":"https://api.github.com/users/giadefa","html_url":"https://github.com/giadefa","followers_url":"https://api.github.com/users/giadefa/followers","following_url":"https://api.github.com/users/giadefa/following{/other_user}","gists_url":"https://api.github.com/users/giadefa/gists{/gist_id}","starred_url":"https://api.github.com/users/giadefa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/giadefa/subscriptions","organizations_url":"https://api.github.com/users/giadefa/orgs","repos_url":"https://api.github.com/users/giadefa/repos","events_url":"https://api.github.com/users/giadefa/events{/privacy}","received_events_url":"https://api.github.com/users/giadefa/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Acellera/htmd/labels/question/discussion","name":"question/discussion","color":"cc317c"}],"state":"open","locked":false,"assignee":{"login":"tonigi","id":2752011,"avatar_url":"https://avatars.githubusercontent.com/u/2752011?v=3","gravatar_id":"","url":"https://api.github.com/users/tonigi","html_url":"https://github.com/tonigi","followers_url":"https://api.github.com/users/tonigi/followers","following_url":"https://api.github.com/users/tonigi/following{/other_user}","gists_url":"https://api.github.com/users/tonigi/gists{/gist_id}","starred_url":"https://api.github.com/users/tonigi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tonigi/subscriptions","organizations_url":"https://api.github.com/users/tonigi/orgs","repos_url":"https://api.github.com/users/tonigi/repos","events_url":"https://api.github.com/users/tonigi/events{/privacy}","received_events_url":"https://api.github.com/users/tonigi/received_events","type":"User","site_admin":false},"assignees":[{"login":"tonigi","id":2752011,"avatar_url":"https://avatars.githubusercontent.com/u/2752011?v=3","gravatar_id":"","url":"https://api.github.com/users/tonigi","html_url":"https://github.com/tonigi","followers_url":"https://api.github.com/users/tonigi/followers","following_url":"https://api.github.com/users/tonigi/following{/other_user}","gists_url":"https://api.github.com/users/tonigi/gists{/gist_id}","starred_url":"https://api.github.com/users/tonigi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tonigi/subscriptions","organizations_url":"https://api.github.com/users/tonigi/orgs","repos_url":"https://api.github.com/users/tonigi/repos","events_url":"https://api.github.com/users/tonigi/events{/privacy}","received_events_url":"https://api.github.com/users/tonigi/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2016-06-30T00:52:02Z","updated_at":"2016-06-30T09:14:18Z","closed_at":null,"body":"If I run this code\r\n```\r\nprotein = Molecule('2OV5')\r\nprotein.filter('chain A and (protein or water)')  # can I keep water if I use proteinPrepare?\r\nprotein_prep, report = proteinPrepare(protein,returnDetails=True)\r\n\r\n2016-06-30 02:40:22,403 - htmd.molecule.molecule - INFO - Attempting PDB query for 2OV5\r\n2016-06-30 02:40:25,485 - htmd.molecule.molecule - INFO - Removed 4094 atoms. 2080 atoms remaining in the molecule.\r\n2016-06-30 02:40:25,676 - propka - INFO - No pdbfile provided\r\n2016-06-30 02:40:35,088 - htmd.builder.residuedata - WARNING - Dubious protonation state: the pKa of 3 residues is within 1.0 units of pH 7.0.\r\n2016-06-30 02:40:35,092 - htmd.builder.residuedata - WARNING - Dubious protonation state:    HIS 219  A\r\n2016-06-30 02:40:35,092 - htmd.builder.residuedata - WARNING - Dubious protonation state:    LYS 234  A\r\n2016-06-30 02:40:35,093 - htmd.builder.residuedata - WARNING - Dubious protonation state:    N+ 30  A\r\n```\r\n\r\n* why propka complains of no pdbfile?\r\n* resid 30 is actally alanine, no N+?\r\n\r\n```\r\nreport.data[report.data.resid==219]\r\n\r\nresname\tresid\tinsertion\tchain\tpKa\tprotonation\tflipped\tpatches\tburied\tz\tmembraneExposed\tpka_group_id\tpka_residue_type\tpka_type\tpka_charge\tpka_atom_name\tpka_atom_sybyl_type\r\n188\tHIS\t219\t\tA\t6.510094\tHIE\tFalse\t[PEPTIDE]\t0.0\t9.923\tNaN\t43.0\tHIS\tHIS\t1\tCG\t\r\n```\r\n* actually HIS 219 looking at the crystal water structure should probably be protonated but it does not. Does propka looks at water  as well? Because the result is the same with and without passing water\r\n\r\n* these NAN are errors ?\r\n"},"comment":{"url":"https://api.github.com/repos/Acellera/htmd/issues/comments/229605790","html_url":"https://github.com/Acellera/htmd/issues/76#issuecomment-229605790","issue_url":"https://api.github.com/repos/Acellera/htmd/issues/76","id":229605790,"user":{"login":"tonigi","id":2752011,"avatar_url":"https://avatars.githubusercontent.com/u/2752011?v=3","gravatar_id":"","url":"https://api.github.com/users/tonigi","html_url":"https://github.com/tonigi","followers_url":"https://api.github.com/users/tonigi/followers","following_url":"https://api.github.com/users/tonigi/following{/other_user}","gists_url":"https://api.github.com/users/tonigi/gists{/gist_id}","starred_url":"https://api.github.com/users/tonigi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tonigi/subscriptions","organizations_url":"https://api.github.com/users/tonigi/orgs","repos_url":"https://api.github.com/users/tonigi/repos","events_url":"https://api.github.com/users/tonigi/events{/privacy}","received_events_url":"https://api.github.com/users/tonigi/received_events","type":"User","site_admin":false},"created_at":"2016-06-30T09:14:17Z","updated_at":"2016-06-30T09:14:17Z","body":"> Does propka looks at water as well? \r\n\r\nNo, propKa doesn't consider water as far as I know. pdb2pqr does, but after the protonation decision is taken.  Note that the warning message is already telling you that the protonation is not to be trusted (borderline with pH).\r\n\r\n> resid 30 is actally alanine, no N+?\r\n\r\nTerminals have their own pKa values, independent of the sidechain of the corresponding residue. They are called N+ and C-. Feel free to ignore them if you are capping.\r\n\r\n> Why propka complains of no pdbfile?\r\n\r\nA useless log messages in propka upstream code, but I would not like to fork the code for minor things.\r\n\r\n> these NAN are errors ?\r\n\r\nNo, just \"not applicable\", but things like NA or empty are not allowed in float columns.\r\n\r\n"}}
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