{"action":"created","issue":{"url":"https://api.github.com/repos/cryoem/eman2/issues/256","repository_url":"https://api.github.com/repos/cryoem/eman2","labels_url":"https://api.github.com/repos/cryoem/eman2/issues/256/labels{/name}","comments_url":"https://api.github.com/repos/cryoem/eman2/issues/256/comments","events_url":"https://api.github.com/repos/cryoem/eman2/issues/256/events","html_url":"https://github.com/cryoem/eman2/pull/256","id":365965059,"node_id":"MDExOlB1bGxSZXF1ZXN0MjE5NzU1OTA2","number":256,"title":"added normalized output volume","user":{"login":"taputechnic","id":12241752,"node_id":"MDQ6VXNlcjEyMjQxNzUy","avatar_url":"https://avatars0.githubusercontent.com/u/12241752?v=4","gravatar_id":"","url":"https://api.github.com/users/taputechnic","html_url":"https://github.com/taputechnic","followers_url":"https://api.github.com/users/taputechnic/followers","following_url":"https://api.github.com/users/taputechnic/following{/other_user}","gists_url":"https://api.github.com/users/taputechnic/gists{/gist_id}","starred_url":"https://api.github.com/users/taputechnic/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/taputechnic/subscriptions","organizations_url":"https://api.github.com/users/taputechnic/orgs","repos_url":"https://api.github.com/users/taputechnic/repos","events_url":"https://api.github.com/users/taputechnic/events{/privacy}","received_events_url":"https://api.github.com/users/taputechnic/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-10-02T15:53:03Z","updated_at":"2018-10-02T16:57:09Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/cryoem/eman2/pulls/256","html_url":"https://github.com/cryoem/eman2/pull/256","diff_url":"https://github.com/cryoem/eman2/pull/256.diff","patch_url":"https://github.com/cryoem/eman2/pull/256.patch"},"body":"The PostRefiner now solicits the mask threshold in units of sigma. I normalized the volume so that the threshold you find in Chimera corresponds to the PostRefiner threshold."},"comment":{"url":"https://api.github.com/repos/cryoem/eman2/issues/comments/426350226","html_url":"https://github.com/cryoem/eman2/pull/256#issuecomment-426350226","issue_url":"https://api.github.com/repos/cryoem/eman2/issues/256","id":426350226,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNjM1MDIyNg==","user":{"login":"mstabrin","id":18047816,"node_id":"MDQ6VXNlcjE4MDQ3ODE2","avatar_url":"https://avatars1.githubusercontent.com/u/18047816?v=4","gravatar_id":"","url":"https://api.github.com/users/mstabrin","html_url":"https://github.com/mstabrin","followers_url":"https://api.github.com/users/mstabrin/followers","following_url":"https://api.github.com/users/mstabrin/following{/other_user}","gists_url":"https://api.github.com/users/mstabrin/gists{/gist_id}","starred_url":"https://api.github.com/users/mstabrin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mstabrin/subscriptions","organizations_url":"https://api.github.com/users/mstabrin/orgs","repos_url":"https://api.github.com/users/mstabrin/repos","events_url":"https://api.github.com/users/mstabrin/events{/privacy}","received_events_url":"https://api.github.com/users/mstabrin/received_events","type":"User","site_admin":false},"created_at":"2018-10-02T16:57:09Z","updated_at":"2018-10-02T16:57:09Z","author_association":"CONTRIBUTOR","body":"Hello Pawel,\r\n\r\nthis changed happened in response to the change of the mask threshold change in the PostRefiner: https://github.com/cryoem/eman2/commit/d7eb986ec9606c283cbc90bee4182ae6e7696cb6\r\n\r\nSince the change was coming from your lab, we thought you want to go in this direction and in terms of automation, this makes actually a lot of sense.  \r\nHowever, the user needs to have a volume to check the threshold in chimera, so we decided to add just one small output file to meridien instead of introducing a whole new command that needs to have a separate step in the GUI.\r\nThis also means, that this normalized volume is used every time before post refining, so rarely used is not quite correct.\r\n\r\nWe will work on a way to cleanup the directories after an successful run.\r\n\r\nbest,\r\nMarkus\r\n"}}
{"actor":{"display_login":"mstabrin"}}