{"action":"created","issue":{"url":"https://api.github.com/repos/I2PC/scipion/issues/323","repository_url":"https://api.github.com/repos/I2PC/scipion","labels_url":"https://api.github.com/repos/I2PC/scipion/issues/323/labels{/name}","comments_url":"https://api.github.com/repos/I2PC/scipion/issues/323/comments","events_url":"https://api.github.com/repos/I2PC/scipion/issues/323/events","html_url":"https://github.com/I2PC/scipion/issues/323","id":134356332,"number":323,"title":"Bug of Detector pixel size in Relion star files","user":{"login":"delarosatrevin","id":8441688,"avatar_url":"https://avatars.githubusercontent.com/u/8441688?v=3","gravatar_id":"","url":"https://api.github.com/users/delarosatrevin","html_url":"https://github.com/delarosatrevin","followers_url":"https://api.github.com/users/delarosatrevin/followers","following_url":"https://api.github.com/users/delarosatrevin/following{/other_user}","gists_url":"https://api.github.com/users/delarosatrevin/gists{/gist_id}","starred_url":"https://api.github.com/users/delarosatrevin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/delarosatrevin/subscriptions","organizations_url":"https://api.github.com/users/delarosatrevin/orgs","repos_url":"https://api.github.com/users/delarosatrevin/repos","events_url":"https://api.github.com/users/delarosatrevin/events{/privacy}","received_events_url":"https://api.github.com/users/delarosatrevin/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/I2PC/scipion/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/I2PC/scipion/labels/in%20progress","name":"in progress","color":"ededed"}],"state":"closed","locked":false,"assignee":{"login":"delarosatrevin","id":8441688,"avatar_url":"https://avatars.githubusercontent.com/u/8441688?v=3","gravatar_id":"","url":"https://api.github.com/users/delarosatrevin","html_url":"https://github.com/delarosatrevin","followers_url":"https://api.github.com/users/delarosatrevin/followers","following_url":"https://api.github.com/users/delarosatrevin/following{/other_user}","gists_url":"https://api.github.com/users/delarosatrevin/gists{/gist_id}","starred_url":"https://api.github.com/users/delarosatrevin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/delarosatrevin/subscriptions","organizations_url":"https://api.github.com/users/delarosatrevin/orgs","repos_url":"https://api.github.com/users/delarosatrevin/repos","events_url":"https://api.github.com/users/delarosatrevin/events{/privacy}","received_events_url":"https://api.github.com/users/delarosatrevin/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/I2PC/scipion/milestones/3","html_url":"https://github.com/I2PC/scipion/milestones/v1.0.1","labels_url":"https://api.github.com/repos/I2PC/scipion/milestones/3/labels","id":1583545,"number":3,"title":"v1.0.1","description":"First bug fixes release after the v1.0.0","creator":{"login":"delarosatrevin","id":8441688,"avatar_url":"https://avatars.githubusercontent.com/u/8441688?v=3","gravatar_id":"","url":"https://api.github.com/users/delarosatrevin","html_url":"https://github.com/delarosatrevin","followers_url":"https://api.github.com/users/delarosatrevin/followers","following_url":"https://api.github.com/users/delarosatrevin/following{/other_user}","gists_url":"https://api.github.com/users/delarosatrevin/gists{/gist_id}","starred_url":"https://api.github.com/users/delarosatrevin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/delarosatrevin/subscriptions","organizations_url":"https://api.github.com/users/delarosatrevin/orgs","repos_url":"https://api.github.com/users/delarosatrevin/repos","events_url":"https://api.github.com/users/delarosatrevin/events{/privacy}","received_events_url":"https://api.github.com/users/delarosatrevin/received_events","type":"User","site_admin":false},"open_issues":1,"closed_issues":3,"state":"open","created_at":"2016-02-15T15:08:04Z","updated_at":"2016-02-19T08:18:42Z","due_on":"2016-03-31T22:00:00Z","closed_at":null},"comments":4,"created_at":"2016-02-17T18:11:58Z","updated_at":"2016-02-19T08:18:42Z","closed_at":"2016-02-19T08:18:42Z","body":"Reported by @azazellochg\n\nI have noticed that in scipion-produced relion star files (after 2d classification relion protocol) the_rlnMagnification column is wrong (it prints nominal 59000 instead of actual 31818) and there is no _rlnDetectorPixelSize column in output star files. \n\nThat's why I wonder what values should be used for Magnification during Micrograph import protocol? \n\nI have used 59000x and 1.1A/px (\"from image\") during import. Classification was done on C4 data, hence pixel size 4.4A. Actual mag should be then 4.4/14um=31818 and not 59000 in star file, given our detector size 14um."},"comment":{"url":"https://api.github.com/repos/I2PC/scipion/issues/comments/186113932","html_url":"https://github.com/I2PC/scipion/issues/323#issuecomment-186113932","issue_url":"https://api.github.com/repos/I2PC/scipion/issues/323","id":186113932,"user":{"login":"delarosatrevin","id":8441688,"avatar_url":"https://avatars.githubusercontent.com/u/8441688?v=3","gravatar_id":"","url":"https://api.github.com/users/delarosatrevin","html_url":"https://github.com/delarosatrevin","followers_url":"https://api.github.com/users/delarosatrevin/followers","following_url":"https://api.github.com/users/delarosatrevin/following{/other_user}","gists_url":"https://api.github.com/users/delarosatrevin/gists{/gist_id}","starred_url":"https://api.github.com/users/delarosatrevin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/delarosatrevin/subscriptions","organizations_url":"https://api.github.com/users/delarosatrevin/orgs","repos_url":"https://api.github.com/users/delarosatrevin/repos","events_url":"https://api.github.com/users/delarosatrevin/events{/privacy}","received_events_url":"https://api.github.com/users/delarosatrevin/received_events","type":"User","site_admin":false},"created_at":"2016-02-19T08:18:42Z","updated_at":"2016-02-19T08:18:42Z","body":"It seems that we are doing this correctly. Since in Relion you could either pass magnification and detector pixel size OR the --angpix. Since in our case we are not passing the detector pixel size, everything should work as expected. It is not clear to me if there is a preferred way for Relion.\r\nSo I will close this issue for the moment."}}