{"action":"created","issue":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/601","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/601/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/601/comments","events_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/601/events","html_url":"https://github.com/markovmodel/PyEMMA/issues/601","id":114301994,"number":601,"title":"Fluxes on coarse-grained model","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},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-10-30T16:16:44Z","updated_at":"2015-10-30T16:26:49Z","closed_at":null,"body":"Hi, I was looking at your tutorial for Benzamidine and I wanted to try the fluxes plot at the end. \r\nI am however not using a HMM, I am using a normal MSM with pcca.\r\nIt seems that msm.tpt given my normal MSM calculates the fluxes between microstates not macrostates. Also it does not have an option to calculate the fluxes between macrostates. \r\nSo I assume msm.tpt only gives macrostate fluxes when given an HMSM?"},"comment":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/comments/152577334","html_url":"https://github.com/markovmodel/PyEMMA/issues/601#issuecomment-152577334","issue_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/601","id":152577334,"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":"2015-10-30T16:26:49Z","updated_at":"2015-10-30T16:26:49Z","body":"Ah perfect, I was looking for an option in msm.tpt not in its result.\nThanks!\n\nOn Fri, Oct 30, 2015 at 5:22 PM, Guillermo Pérez-Hernández <\nnotifications@github.com> wrote:\n\n> Hi Stefan,\n>\n> you can coarse grain the tpt object on the pcca sets.\n>\n>\n> http://www.emma-project.org/latest/api/generated/msmtools.flux.ReactiveFlux.html#msmtools.flux.ReactiveFlux.coarse_grain\n>\n> On 10/30/2015 05:16 PM, Stefan wrote:\n> > Hi, I was looking at your tutorial for Benzamidine and I wanted to try\n> > the fluxes plot at the end.\n> > I am however not using a HMM, I am using a normal MSM with pcca.\n> > It seems that msm.tpt given my normal MSM calculates the fluxes between\n> > microstates not macrostates. Also it does not have an option to\n> > calculate the fluxes between macrostates.\n> > So I assume msm.tpt only gives macrostate fluxes when given an HMSM?\n> >\n> > —\n> > Reply to this email directly or view it on GitHub\n> > <https://github.com/markovmodel/PyEMMA/issues/601>.\n> >\n>\n> --\n> Dr. Guillermo Pérez-Hernández\n> Freie Universität Berlin\n> Institute for Mathematics\n> Arnimallee 6\n> D-14195 Berlin\n> tel 0049 30 838 75775\n> http://userpage.fu-berlin.de/gph82/\n> --\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/markovmodel/PyEMMA/issues/601#issuecomment-152574600>.\n>\n"}}