{"action":"opened","number":1707,"pull_request":{"url":"https://api.github.com/repos/I2PC/scipion/pulls/1707","id":205055837,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA1MDU1ODM3","html_url":"https://github.com/I2PC/scipion/pull/1707","diff_url":"https://github.com/I2PC/scipion/pull/1707.diff","patch_url":"https://github.com/I2PC/scipion/pull/1707.patch","issue_url":"https://api.github.com/repos/I2PC/scipion/issues/1707","number":1707,"state":"open","locked":false,"title":"Model 10 superpose pdbs","user":{"login":"mmmtnez","id":7781101,"node_id":"MDQ6VXNlcjc3ODExMDE=","avatar_url":"https://avatars3.githubusercontent.com/u/7781101?v=4","gravatar_id":"","url":"https://api.github.com/users/mmmtnez","html_url":"https://github.com/mmmtnez","followers_url":"https://api.github.com/users/mmmtnez/followers","following_url":"https://api.github.com/users/mmmtnez/following{/other_user}","gists_url":"https://api.github.com/users/mmmtnez/gists{/gist_id}","starred_url":"https://api.github.com/users/mmmtnez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mmmtnez/subscriptions","organizations_url":"https://api.github.com/users/mmmtnez/orgs","repos_url":"https://api.github.com/users/mmmtnez/repos","events_url":"https://api.github.com/users/mmmtnez/events{/privacy}","received_events_url":"https://api.github.com/users/mmmtnez/received_events","type":"User","site_admin":false},"body":"Dear all,\r\n\r\nhere you are this new pull request model_10_superpose_pdbs that includes:\r\n\r\n1.- A new phenix package-derived protocol/tool to handle pdbs (protocol_superpose_pdbs). It allows to superpose a couple of atomic structures (pdbs or cifs) (fixed and moving) to ensure the optimal matching. RMSD between these two pdbs at the beginning (start) and at the end (final) of matching assess the similarity between both structures. RMSD values are showed in the summary panel of SCIPION. Viewer and test for this protocol have been also included. Test for this part:\r\nscipion test em.packages.phenix.tests.test_protocol_superpose_pdbs.TestProtSuperposePdbs\r\n\r\n2.- Individual tests for programs that had previously tests in the modeling workflow (test_workflow_modeling) in order to have also specific tests for ccp4, chimera and phenix packages considering potential future plugins. Test for this part:\r\nscipion test em.packages.ccp4.tests.test_protocol_coot_refmac.TestCootRefinement2\r\nscipion test em.packages.ccp4.tests.test_protocol_coot_refmac.TestRefmacRefinement2\r\nscipion test em.packages.chimera.tests.test_protocol_chimera_fit.TestChimeraFit2\r\nscipion test em.packages.phenix.tests.test_protocol_emringer.TestEMRingerValidation2\r\n\r\n3.- Modifications in some tests included in the modeling workflow to include changes in ccp4 protocols (coot and refmac) showed below. Tests for this part:\r\nscipion test tests.em.workflows.test_workflow_modeling.TestCootRefinement\r\nscipion test tests.em.workflows.test_workflow_modeling.TestRefmacRefinement\r\nscipion test tests.em.workflows.test_workflow_modeling.TestEMRingerValidation\r\n\r\n4.- Modifications in the ccp4 package:\r\n     a) pyworkflow/em/packages/ccp4/convert.py: Inclusion of valid CCP4 version.\r\n     b)  pyworkflow/em/packages/ccp4/protocol_coot.py: Inclusion of a database (in the extra folder) to save coot outputs, and inclusion of the option of adding a label associated to each generated pdb that will be saved by coot scipion_write().\r\n    c) pyworkflow/em/packages/ccp4/protocol_refmac.py (and respective protocol templates): Inclusion of the option to have the mask of the atomic structure that has to be refined. Modification to get a functional protocol with cif files of atomic structures.\r\n   d) coot and refmac viewers have been also modified according to new protocols.\r\n\r\n5.- Modifications in the phenix package:\r\n    a) pyworkflow/em/packages/phenix/convert.py: Inclusion of an additional path to execute phenix programs. This new path is needed  to run superpose_pdbs and real_space_refine phenix programs, whereas emringer and molprobity run with the already existing path. pyworkflow/em/packages/phenix/protocol_emringer.py has been also modified according with this last change.\r\n\r\n\r\n","created_at":"2018-07-31T09:50:24Z","updated_at":"2018-07-31T09:50:24Z","closed_at":null,"merged_at":null,"merge_commit_sha":null,"assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/I2PC/scipion/pulls/1707/commits","review_comments_url":"https://api.github.com/repos/I2PC/scipion/pulls/1707/comments","review_comment_url":"https://api.github.com/repos/I2PC/scipion/pulls/comments{/number}","comments_url":"https://api.github.com/repos/I2PC/scipion/issues/1707/comments","statuses_url":"https://api.github.com/repos/I2PC/scipion/statuses/ed36273dc5e6652e25c7f41406cc5c53737396a4","head":{"label":"mmmtnez:model_10_superpose_pdbs","ref":"model_10_superpose_pdbs","sha":"ed36273dc5e6652e25c7f41406cc5c53737396a4","user":{"login":"mmmtnez","id":7781101,"node_id":"MDQ6VXNlcjc3ODExMDE=","avatar_url":"https://avatars3.githubusercontent.com/u/7781101?v=4","gravatar_id":"","url":"https://api.github.com/users/mmmtnez","html_url":"https://github.com/mmmtnez","followers_url":"https://api.github.com/users/mmmtnez/followers","following_url":"https://api.github.com/users/mmmtnez/following{/other_user}","gists_url":"https://api.github.com/users/mmmtnez/gists{/gist_id}","starred_url":"https://api.github.com/users/mmmtnez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mmmtnez/subscriptions","organizations_url":"https://api.github.com/users/mmmtnez/orgs","repos_url":"https://api.github.com/users/mmmtnez/repos","events_url":"https://api.github.com/users/mmmtnez/events{/privacy}","received_events_url":"https://api.github.com/users/mmmtnez/received_events","type":"User","site_admin":false},"repo":{"id":119827792,"node_id":"MDEwOlJlcG9zaXRvcnkxMTk4Mjc3OTI=","name":"scipion","full_name":"mmmtnez/scipion","owner":{"login":"mmmtnez","id":7781101,"node_id":"MDQ6VXNlcjc3ODExMDE=","avatar_url":"https://avatars3.githubusercontent.com/u/7781101?v=4","gravatar_id":"","url":"https://api.github.com/users/mmmtnez","html_url":"https://github.com/mmmtnez","followers_url":"https://api.github.com/users/mmmtnez/followers","following_url":"https://api.github.com/users/mmmtnez/following{/other_user}","gists_url":"https://api.github.com/users/mmmtnez/gists{/gist_id}","starred_url":"https://api.github.com/users/mmmtnez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mmmtnez/subscriptions","organizations_url":"https://api.github.com/users/mmmtnez/orgs","repos_url":"https://api.github.com/users/mmmtnez/repos","events_url":"https://api.github.com/users/mmmtnez/events{/privacy}","received_events_url":"https://api.github.com/users/mmmtnez/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/mmmtnez/scipion","description":"Scipion 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