{"action":"created","issue":{"url":"https://api.github.com/repos/arose/ngl/issues/47","repository_url":"https://api.github.com/repos/arose/ngl","labels_url":"https://api.github.com/repos/arose/ngl/issues/47/labels{/name}","comments_url":"https://api.github.com/repos/arose/ngl/issues/47/comments","events_url":"https://api.github.com/repos/arose/ngl/issues/47/events","html_url":"https://github.com/arose/ngl/issues/47","id":129103866,"number":47,"title":"no bond for modified nucleotide","user":{"login":"hainm","id":4451957,"avatar_url":"https://avatars.githubusercontent.com/u/4451957?v=3","gravatar_id":"","url":"https://api.github.com/users/hainm","html_url":"https://github.com/hainm","followers_url":"https://api.github.com/users/hainm/followers","following_url":"https://api.github.com/users/hainm/following{/other_user}","gists_url":"https://api.github.com/users/hainm/gists{/gist_id}","starred_url":"https://api.github.com/users/hainm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hainm/subscriptions","organizations_url":"https://api.github.com/users/hainm/orgs","repos_url":"https://api.github.com/users/hainm/repos","events_url":"https://api.github.com/users/hainm/events{/privacy}","received_events_url":"https://api.github.com/users/hainm/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/arose/ngl/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/arose/ngl/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-01-27T10:45:07Z","updated_at":"2016-08-26T19:01:15Z","closed_at":null,"body":"Please check this\r\n\r\n```python\r\nimport pytraj as pt\r\nimport nglview as nv\r\n\r\ntraj = pt.load('f2.pdb')\r\nview = nv.show_pytraj(traj)\r\nview.representations = []\r\nview.add_representation('licorice')\r\nview\r\n```\r\n\r\n![picture1](https://cloud.githubusercontent.com/assets/4451957/12610995/99ef39f6-c4b8-11e5-9e6a-446f83347120.png)\r\n\r\nfile: https://github.com/hainm/amber_things/blob/master/things/nucleic/f2.pdb\r\n\r\n(modified nucleotides: AF2, GF2).\r\n\r\nDoes ngl has function to guess bond? if not, does it have option to add bond_indices (pytraj has bond info)."},"comment":{"url":"https://api.github.com/repos/arose/ngl/issues/comments/242822915","html_url":"https://github.com/arose/ngl/issues/47#issuecomment-242822915","issue_url":"https://api.github.com/repos/arose/ngl/issues/47","id":242822915,"user":{"login":"arose","id":272250,"avatar_url":"https://avatars.githubusercontent.com/u/272250?v=3","gravatar_id":"","url":"https://api.github.com/users/arose","html_url":"https://github.com/arose","followers_url":"https://api.github.com/users/arose/followers","following_url":"https://api.github.com/users/arose/following{/other_user}","gists_url":"https://api.github.com/users/arose/gists{/gist_id}","starred_url":"https://api.github.com/users/arose/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arose/subscriptions","organizations_url":"https://api.github.com/users/arose/orgs","repos_url":"https://api.github.com/users/arose/repos","events_url":"https://api.github.com/users/arose/events{/privacy}","received_events_url":"https://api.github.com/users/arose/received_events","type":"User","site_admin":false},"created_at":"2016-08-26T19:01:15Z","updated_at":"2016-08-26T19:01:15Z","body":"I think I figured it out, the O2' atoms are replaced by F2' atoms. Handled in 251b481acfd2e8ef9e06652852cb58ffe4532cc6. Do you know/have examples of other common modifications like that?\r\n\r\n![screenshot 24](https://cloud.githubusercontent.com/assets/272250/18017078/94f11438-6b84-11e6-9213-baf3b18158e1.png)\r\n"}}
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