{"action":"created","issue":{"url":"https://api.github.com/repos/mdtraj/mdtraj/issues/874","labels_url":"https://api.github.com/repos/mdtraj/mdtraj/issues/874/labels{/name}","comments_url":"https://api.github.com/repos/mdtraj/mdtraj/issues/874/comments","events_url":"https://api.github.com/repos/mdtraj/mdtraj/issues/874/events","html_url":"https://github.com/mdtraj/mdtraj/issues/874","id":88910956,"number":874,"title":"Removing all atoms but those selected","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":6,"created_at":"2015-06-17T04:47:49Z","updated_at":"2015-06-17T05:41:58Z","closed_at":null,"body":"Forgive my denseness, but the nice [atom selection example notebook](https://github.com/mdtraj/mdtraj/blob/master/examples/atom-selection.ipynb) didn't have an example of deleting all atoms except the ones we were interested in.  Is there an easy way to do this?"},"comment":{"url":"https://api.github.com/repos/mdtraj/mdtraj/issues/comments/112660000","html_url":"https://github.com/mdtraj/mdtraj/issues/874#issuecomment-112660000","issue_url":"https://api.github.com/repos/mdtraj/mdtraj/issues/874","id":112660000,"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},"created_at":"2015-06-17T05:41:58Z","updated_at":"2015-06-17T05:41:58Z","body":"I'm struggling to try to figure out how to make an mdtraj `Trajectory` object from OpenMM `topology` and `positions` object.  The obvious idiom doesn't seem to work:\r\n```\r\nmdtraj.Trajectory(xyz=fixer.positions, topology=fixer.topology) \r\n```\r\nMaybe it would be worthwhile to have an example if this in the docs too?"}}