{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/ensembler/issues/70","repository_url":"https://api.github.com/repos/choderalab/ensembler","labels_url":"https://api.github.com/repos/choderalab/ensembler/issues/70/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/ensembler/issues/70/comments","events_url":"https://api.github.com/repos/choderalab/ensembler/issues/70/events","html_url":"https://github.com/choderalab/ensembler/issues/70","id":145393562,"number":70,"title":"Proposing improvements to quickmodel command line arguments","user":{"login":"rafwiewiora","id":12088757,"avatar_url":"https://avatars.githubusercontent.com/u/12088757?v=3","gravatar_id":"","url":"https://api.github.com/users/rafwiewiora","html_url":"https://github.com/rafwiewiora","followers_url":"https://api.github.com/users/rafwiewiora/followers","following_url":"https://api.github.com/users/rafwiewiora/following{/other_user}","gists_url":"https://api.github.com/users/rafwiewiora/gists{/gist_id}","starred_url":"https://api.github.com/users/rafwiewiora/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rafwiewiora/subscriptions","organizations_url":"https://api.github.com/users/rafwiewiora/orgs","repos_url":"https://api.github.com/users/rafwiewiora/repos","events_url":"https://api.github.com/users/rafwiewiora/events{/privacy}","received_events_url":"https://api.github.com/users/rafwiewiora/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2016-04-02T16:53:13Z","updated_at":"2016-04-04T21:29:04Z","closed_at":null,"body":"@jchodera \r\n\r\nPasting from Slack:\r\n\r\n>About the code question - what I meant is, in words what I want Ensembler to do here is - look at   Uniprot protein code Q9NQR1 - take the sequence of that protein and use that as target & take all PDB structures listed for that protein and use them as templates; align and model and much sequence as is possible with these inputs\r\n\r\n >[12:43] \r\n so the only user input I made here is really the Uniprot code\r\n \r\n>[12:43] \r\nwhich is why I’m a bit surprised I have to write it out as this `ensembler quickmodel --target_uniprot_entry_name \"SETD8_HUMAN\" --template_uniprot_query \"accession:q9nqr1\" --no-loopmodel --uniprot_domain_regex \"SET\"`\r\n\r\n>john.chodera [12:44 PM] \r\nIf you try to model a multidomain protein with ensembler it will likely give you garbage\r\n\r\n>[12:44] \r\nAre you asking if we could just make `--uniprot_domain_regex <regex>` optional if you want the whole thing?\r\n\r\n>[12:44] \r\nAnd maybe `--template_uniprot_query` should also default to the `target_uniprot_entry_name` first variant?\r\n\r\n>[12:45] \r\nThose sound like reasonable behaviors.\r\n\r\n>[12:45] \r\nMaybe open an issue to suggest these, and we can see how feasible that is?\r\n\r\n>\r\nrafwiewiora [12:49 PM] \r\nThe domain regex is fine - yeah, I get the potential problems - no problems here even though the Uniprot sequence is not limited to SET domain, but all but 1 templates are only the SET domain - so I think within the full pipeline i managed to not specify the domain and Modeller got it right - but I guess the problems would arise if the templates have different sequence coverages. So that’s fine!\r\n\r\n>But yeah the `—template_uniprot_query' and `—target_uniprot_entry_name` are specifying the same thing, but in 2 different ways - that is very confusing I think, so I would suggest:\r\na) Allowing using the same thing for both + default same would be nice\r\nb) I was also confused about the other arguments `—targetids` and `templateids`, they sounds like the Uniprot code should be passed, but in fact they’re names of folders containing targets and templates in the project folder if they exist already right? So that had me trapped for a moment - first thing I’m going to write more docs for. Should we just have a ‘target_and_template_uniprot_code` or something like that?\r\n"},"comment":{"url":"https://api.github.com/repos/choderalab/ensembler/issues/comments/205504249","html_url":"https://github.com/choderalab/ensembler/issues/70#issuecomment-205504249","issue_url":"https://api.github.com/repos/choderalab/ensembler/issues/70","id":205504249,"user":{"login":"rafwiewiora","id":12088757,"avatar_url":"https://avatars.githubusercontent.com/u/12088757?v=3","gravatar_id":"","url":"https://api.github.com/users/rafwiewiora","html_url":"https://github.com/rafwiewiora","followers_url":"https://api.github.com/users/rafwiewiora/followers","following_url":"https://api.github.com/users/rafwiewiora/following{/other_user}","gists_url":"https://api.github.com/users/rafwiewiora/gists{/gist_id}","starred_url":"https://api.github.com/users/rafwiewiora/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rafwiewiora/subscriptions","organizations_url":"https://api.github.com/users/rafwiewiora/orgs","repos_url":"https://api.github.com/users/rafwiewiora/repos","events_url":"https://api.github.com/users/rafwiewiora/events{/privacy}","received_events_url":"https://api.github.com/users/rafwiewiora/received_events","type":"User","site_admin":false},"created_at":"2016-04-04T21:29:04Z","updated_at":"2016-04-04T21:29:04Z","body":"Ok cool, will do! Thanks Danny!"}}