{"action":"opened","issue":{"url":"https://api.github.com/repos/ihmwg/IHM-dictionary/issues/73","repository_url":"https://api.github.com/repos/ihmwg/IHM-dictionary","labels_url":"https://api.github.com/repos/ihmwg/IHM-dictionary/issues/73/labels{/name}","comments_url":"https://api.github.com/repos/ihmwg/IHM-dictionary/issues/73/comments","events_url":"https://api.github.com/repos/ihmwg/IHM-dictionary/issues/73/events","html_url":"https://github.com/ihmwg/IHM-dictionary/issues/73","id":367829539,"node_id":"MDU6SXNzdWUzNjc4Mjk1Mzk=","number":73,"title":"Add pseudo-atoms support to define restraints","user":{"login":"mtrellet","id":715654,"node_id":"MDQ6VXNlcjcxNTY1NA==","avatar_url":"https://avatars0.githubusercontent.com/u/715654?v=4","gravatar_id":"","url":"https://api.github.com/users/mtrellet","html_url":"https://github.com/mtrellet","followers_url":"https://api.github.com/users/mtrellet/followers","following_url":"https://api.github.com/users/mtrellet/following{/other_user}","gists_url":"https://api.github.com/users/mtrellet/gists{/gist_id}","starred_url":"https://api.github.com/users/mtrellet/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mtrellet/subscriptions","organizations_url":"https://api.github.com/users/mtrellet/orgs","repos_url":"https://api.github.com/users/mtrellet/repos","events_url":"https://api.github.com/users/mtrellet/events{/privacy}","received_events_url":"https://api.github.com/users/mtrellet/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-10-08T14:56:28Z","updated_at":"2018-10-08T14:56:28Z","closed_at":null,"author_association":"NONE","body":"In some of HADDOCK protocols, we make use of pseudo-atoms to define distance restraints between either other pseudo-atoms matching geometrical features of a molecule (center of mass for instance) or atom/residues of the molecular partners.\r\n\r\nThis is, for instance, the case in the HADDOCK-EM protocol at the rigid-body minimization stage (it0) as described below.\r\n\r\n<img width=\"1327\" alt=\"screen shot 2018-09-17 at 16 19 51\" src=\"https://user-images.githubusercontent.com/715654/46616051-021f6400-cb1a-11e8-8430-c95734dc9cfb.png\">\r\n\r\nIf part of the definition of pseudo-atoms is made within the protocol and then does not mandatorily require to be present in a mmCIF file, the centroid coordinates used in the HADDOCK-EM protocol, and obtained via a fitting of the molecular structures in a density map, are provided as input by the users. For the sake of exhaustiveness, it would be interesting to be able to add them in the IHM dictionary and be able to list them in the `poly_atom_feature` section to be further referenced in `derived_distance_restraints`."}}
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