{"action":"created","issue":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/772","repository_url":"https://api.github.com/repos/ParmEd/ParmEd","labels_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/772/labels{/name}","comments_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/772/comments","events_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/772/events","html_url":"https://github.com/ParmEd/ParmEd/issues/772","id":186625922,"number":772,"title":"does not recognize alternative atoms in phenix atom order","user":{"login":"hainm","id":4451957,"avatar_url":"https://avatars.githubusercontent.com/u/4451957?v=3","gravatar_id":"","url":"https://api.github.com/users/hainm","html_url":"https://github.com/hainm","followers_url":"https://api.github.com/users/hainm/followers","following_url":"https://api.github.com/users/hainm/following{/other_user}","gists_url":"https://api.github.com/users/hainm/gists{/gist_id}","starred_url":"https://api.github.com/users/hainm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hainm/subscriptions","organizations_url":"https://api.github.com/users/hainm/orgs","repos_url":"https://api.github.com/users/hainm/repos","events_url":"https://api.github.com/users/hainm/events{/privacy}","received_events_url":"https://api.github.com/users/hainm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-11-01T19:36:26Z","updated_at":"2016-11-02T18:44:09Z","closed_at":null,"body":"Hi, \r\n\r\nPlease see the output below\r\n```python\r\nimport parmed as pmd\r\n\r\nfn = 'test.pdb'\r\nparm = pmd.load_file(fn)\r\nprint(parm.atoms)\r\n```\r\n\r\nnormal order (ABABAB...)\r\n\r\n```bash\r\nATOM     58  N   VAL     5       4.582  11.380  12.053  1.00 13.28           N\r\nATOM     59  H   VAL     5       3.844  10.863  12.531  1.00 13.28           H\r\nATOM     60  CA  VAL     5       4.579  12.794  12.393  1.00 13.13           C\r\nATOM     61  HA  VAL     5       5.370  13.216  11.772  1.00 13.13           H\r\nATOM     62  CB AVAL     5       3.411  13.602  11.939  0.55 16.58           C\r\nATOM     63  CB BVAL     5       3.101  13.314  12.199  0.45 17.16           C\r\nATOM     64  HB AVAL     5       3.629  14.615  12.277  0.55 17.16           H\r\nATOM     65  HB BVAL     5       2.429  12.830  12.908  0.45 17.16           H\r\nATOM     66  CG1AVAL     5       3.287  13.662  10.423  0.55 16.27           C\r\nATOM     67  CG1BVAL     5       3.035  14.797  12.450  0.45 21.90           C\r\nATOM     68 HG11AVAL     5       2.419  14.263  10.152  0.55 21.90           H\r\nATOM     69 HG11BVAL     5       2.011  15.144  12.313  0.45 21.90           H\r\nATOM     70 HG12AVAL     5       4.186  14.112  10.002  0.55 21.90           H\r\nATOM     71 HG12BVAL     5       3.356  15.008  13.470  0.45 21.90           H\r\nATOM     72 HG13AVAL     5       3.167  12.653  10.028  0.55 21.90           H\r\nATOM     73 HG13BVAL     5       3.690  15.314  11.749  0.45 21.90           H\r\nATOM     74  CG2AVAL     5       2.113  13.231  12.603  0.55 21.87           C\r\nATOM     75  CG2BVAL     5       2.672  12.986  10.766  0.45 18.29           C\r\nATOM     76 HG21AVAL     5       1.314  13.864  12.218  0.55 18.29           H\r\nATOM     77 HG21BVAL     5       1.652  13.335  10.603  0.45 18.29           H\r\nATOM     78 HG22AVAL     5       1.882  12.187  12.392  0.55 18.29           H\r\nATOM     79 HG22BVAL     5       3.342  13.482  10.063  0.45 18.29           H\r\nATOM     80 HG23AVAL     5       2.202  13.373  13.680  0.55 18.29           H\r\nATOM     81 HG23BVAL     5       2.716  11.908  10.611  0.45 18.29           H\r\nATOM     82  C   VAL     5       4.951  13.013  13.840  1.00 12.51           C\r\nATOM     83  O   VAL     5       4.663  12.216  14.725  1.00 18.54           O\r\n```\r\n\r\noutput\r\n```bash\r\nAtomList([\r\n\t<Atom N [0]; In VAL 0>\r\n\t<Atom H [1]; In VAL 0>\r\n\t<Atom CA [2]; In VAL 0>\r\n\t<Atom HA [3]; In VAL 0>\r\n\t<Atom CB [4]; In VAL 0>\r\n\t<Atom HB [5]; In VAL 0>\r\n\t<Atom CG1 [6]; In VAL 0>\r\n\t<Atom HG11 [7]; In VAL 0>\r\n\t<Atom HG12 [8]; In VAL 0>\r\n\t<Atom HG13 [9]; In VAL 0>\r\n\t<Atom CG2 [10]; In VAL 0>\r\n\t<Atom HG21 [11]; In VAL 0>\r\n\t<Atom HG22 [12]; In VAL 0>\r\n\t<Atom HG23 [13]; In VAL 0>\r\n\t<Atom C [14]; In VAL 0>\r\n\t<Atom O [15]; In VAL 0>\r\n])\r\n```"},"comment":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/comments/257961338","html_url":"https://github.com/ParmEd/ParmEd/issues/772#issuecomment-257961338","issue_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/772","id":257961338,"user":{"login":"hainm","id":4451957,"avatar_url":"https://avatars.githubusercontent.com/u/4451957?v=3","gravatar_id":"","url":"https://api.github.com/users/hainm","html_url":"https://github.com/hainm","followers_url":"https://api.github.com/users/hainm/followers","following_url":"https://api.github.com/users/hainm/following{/other_user}","gists_url":"https://api.github.com/users/hainm/gists{/gist_id}","starred_url":"https://api.github.com/users/hainm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hainm/subscriptions","organizations_url":"https://api.github.com/users/hainm/orgs","repos_url":"https://api.github.com/users/hainm/repos","events_url":"https://api.github.com/users/hainm/events{/privacy}","received_events_url":"https://api.github.com/users/hainm/received_events","type":"User","site_admin":false},"created_at":"2016-11-02T18:44:09Z","updated_at":"2016-11-02T18:44:09Z","body":"I just checked: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\r\nand pdb does have both ways. You can search \"exception that residues that have no coordinates, e.g., due to disorder, must appear in SEQRES. \" in that link."}}
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