{"action":"opened","issue":{"url":"https://api.github.com/repos/rcsb/symmetry/issues/47","labels_url":"https://api.github.com/repos/rcsb/symmetry/issues/47/labels{/name}","comments_url":"https://api.github.com/repos/rcsb/symmetry/issues/47/comments","events_url":"https://api.github.com/repos/rcsb/symmetry/issues/47/events","html_url":"https://github.com/rcsb/symmetry/issues/47","id":62626159,"number":47,"title":"CESymmParameters: delete maxNrAlternatives?","user":{"login":"lafita","id":11161522,"avatar_url":"https://avatars.githubusercontent.com/u/11161522?v=3","gravatar_id":"","url":"https://api.github.com/users/lafita","html_url":"https://github.com/lafita","followers_url":"https://api.github.com/users/lafita/followers","following_url":"https://api.github.com/users/lafita/following{/other_user}","gists_url":"https://api.github.com/users/lafita/gists{/gist_id}","starred_url":"https://api.github.com/users/lafita/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lafita/subscriptions","organizations_url":"https://api.github.com/users/lafita/orgs","repos_url":"https://api.github.com/users/lafita/repos","events_url":"https://api.github.com/users/lafita/events{/privacy}","received_events_url":"https://api.github.com/users/lafita/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-03-18T08:42:14Z","updated_at":"2015-03-18T08:42:14Z","closed_at":null,"body":"This parameter is only used in the CeSymm.align method to set the number of iterations that the alignment loop should do (blacking out the previous alignment and doing another iteratively), given that the symmetry order of the protein was known. Was this parameter solely for this purpose, or does it have other functions/meanings? \r\n\r\nIf the maxNrAlternatives is only setting the number of iterations could be deleted, because now the iteration loop is stopped when the TM score and the length of the last alignment drop significantly. With this approach the order of symmetry and thus the number of iterations is set at once, and the parameter is not used anymore.\r\n\r\nFurthermore, another parameter could be introduced to CESymmParameters (named i.e. refineMethod), that specifies the refinement strategy: either the classical strategy with only one alignment or the new one with multiple alignments blacking out iteratively."}}