{"action":"created","issue":{"url":"https://api.github.com/repos/Acellera/htmd/issues/55","repository_url":"https://api.github.com/repos/Acellera/htmd","labels_url":"https://api.github.com/repos/Acellera/htmd/issues/55/labels{/name}","comments_url":"https://api.github.com/repos/Acellera/htmd/issues/55/comments","events_url":"https://api.github.com/repos/Acellera/htmd/issues/55/events","html_url":"https://github.com/Acellera/htmd/issues/55","id":159235388,"number":55,"title":"markovModel(lag,n + 1)","user":{"login":"noeliaferruz","id":12035024,"avatar_url":"https://avatars.githubusercontent.com/u/12035024?v=3","gravatar_id":"","url":"https://api.github.com/users/noeliaferruz","html_url":"https://github.com/noeliaferruz","followers_url":"https://api.github.com/users/noeliaferruz/followers","following_url":"https://api.github.com/users/noeliaferruz/following{/other_user}","gists_url":"https://api.github.com/users/noeliaferruz/gists{/gist_id}","starred_url":"https://api.github.com/users/noeliaferruz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/noeliaferruz/subscriptions","organizations_url":"https://api.github.com/users/noeliaferruz/orgs","repos_url":"https://api.github.com/users/noeliaferruz/repos","events_url":"https://api.github.com/users/noeliaferruz/events{/privacy}","received_events_url":"https://api.github.com/users/noeliaferruz/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Acellera/htmd/labels/question/discussion","name":"question/discussion","color":"cc317c"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-06-08T18:11:26Z","updated_at":"2016-06-08T18:17:17Z","closed_at":null,"body":"Hello!\r\n\r\nQuestion. It seems that sometimes lately when I try to build n macrostates I get n-1, is this an error? \r\n\r\nThanks,\r\nNoelia\r\n\r\n```\r\nmodel=Model(dataTica)\r\n#model.plotTimescales(lags=range(1,100,5))\r\nmodel.markovModel(50,5)\r\nmodel.viewStates(protein=\"protein and name CA\")\r\n\r\n2016-06-07 12:58:55,952 - htmd.model - INFO - 24.4% of the data was used\r\n2016-06-07 12:58:55,959 - htmd.model - INFO - Number of trajectories that visited each macrostate:\r\n2016-06-07 12:58:55,960 - htmd.model - INFO - [5 4 5 2]\r\n2016-06-07 12:58:55,962 - htmd.model - INFO - Take care! Macro 3 has been visited only in 2 trajectories:\r\n2016-06-07 12:58:55,962 - htmd.model - INFO - id = 15\r\nparent = None\r\ninput = []\r\ntrajectory = ['./filtered/e2s6_e1s8p0f473/output.filtered.xtc']\r\nmolfile = ./filtered/filtered.pdb\r\n2016-06-07 12:58:55,963 - htmd.model - INFO - id = 16\r\nparent = None\r\ninput = []\r\ntrajectory = ['./filtered/e2s7_e1s8p0f331/output.filtered.xtc']\r\nmolfile = ./filtered/filtered.pdb\r\n[Parallel(n_jobs=1)]: Done   1 tasks       | elapsed:    6.8s\r\n[Parallel(n_jobs=1)]: Done   2 tasks       | elapsed:   13.9s\r\n[Parallel(n_jobs=1)]: Done   3 tasks       | elapsed:   20.5s\r\n[Parallel(n_jobs=1)]: Done   4 tasks       | elapsed:   27.2s\r\n[Parallel(n_jobs=1)]: Done   4 out of   4 | elapsed:   27.2s finished\r\n```"},"comment":{"url":"https://api.github.com/repos/Acellera/htmd/issues/comments/224681067","html_url":"https://github.com/Acellera/htmd/issues/55#issuecomment-224681067","issue_url":"https://api.github.com/repos/Acellera/htmd/issues/55","id":224681067,"user":{"login":"stefdoerr","id":7935362,"avatar_url":"https://avatars.githubusercontent.com/u/7935362?v=3","gravatar_id":"","url":"https://api.github.com/users/stefdoerr","html_url":"https://github.com/stefdoerr","followers_url":"https://api.github.com/users/stefdoerr/followers","following_url":"https://api.github.com/users/stefdoerr/following{/other_user}","gists_url":"https://api.github.com/users/stefdoerr/gists{/gist_id}","starred_url":"https://api.github.com/users/stefdoerr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stefdoerr/subscriptions","organizations_url":"https://api.github.com/users/stefdoerr/orgs","repos_url":"https://api.github.com/users/stefdoerr/repos","events_url":"https://api.github.com/users/stefdoerr/events{/privacy}","received_events_url":"https://api.github.com/users/stefdoerr/received_events","type":"User","site_admin":false},"created_at":"2016-06-08T18:17:17Z","updated_at":"2016-06-08T18:17:17Z","body":"p.s. there is a new option `units=` where you can provide units for your lag time. So instead of 50 you can do `model.markovModel(5, 5, units='ns')` so that if you later change your fstep you won't accidentally do the analysis on a different lag time."}}
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