{"action":"created","issue":{"url":"https://api.github.com/repos/salilab/pmi/issues/113","labels_url":"https://api.github.com/repos/salilab/pmi/issues/113/labels{/name}","comments_url":"https://api.github.com/repos/salilab/pmi/issues/113/comments","events_url":"https://api.github.com/repos/salilab/pmi/issues/113/events","html_url":"https://github.com/salilab/pmi/issues/113","id":69362035,"number":113,"title":"\"MSE\" residues written as \"HETATM\" are not read correctly in BuildModel function","user":{"login":"procyon777","id":5778776,"avatar_url":"https://avatars.githubusercontent.com/u/5778776?v=3","gravatar_id":"","url":"https://api.github.com/users/procyon777","html_url":"https://github.com/procyon777","followers_url":"https://api.github.com/users/procyon777/followers","following_url":"https://api.github.com/users/procyon777/following{/other_user}","gists_url":"https://api.github.com/users/procyon777/gists{/gist_id}","starred_url":"https://api.github.com/users/procyon777/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/procyon777/subscriptions","organizations_url":"https://api.github.com/users/procyon777/orgs","repos_url":"https://api.github.com/users/procyon777/repos","events_url":"https://api.github.com/users/procyon777/events{/privacy}","received_events_url":"https://api.github.com/users/procyon777/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-04-18T23:57:41Z","updated_at":"2015-05-22T08:37:53Z","closed_at":null,"body":"\"MSE\" residues written as \"HETATM\" in a PDB file (i.e. 3PBP and 1XIP) are not read correctly in the BuildModel function of PMI macro.py.  Instead of reading their coordinates from the PDB file, the BuildModel function treats each \"MSE\" residue as an unknown residue, thus placing a flexible bead there.\r\n\r\nCurrently my solution is replacing \"MSE\" with the standard \"MET\" and \"HETATM\" with \"ATOM\" manually in the PDB file.  However, PMI should eventually read the coordinates of \"MSE\" written as \"HETATM\" correctly."},"comment":{"url":"https://api.github.com/repos/salilab/pmi/issues/comments/104571726","html_url":"https://github.com/salilab/pmi/issues/113#issuecomment-104571726","issue_url":"https://api.github.com/repos/salilab/pmi/issues/113","id":104571726,"user":{"login":"Pellarin","id":2477712,"avatar_url":"https://avatars.githubusercontent.com/u/2477712?v=3","gravatar_id":"","url":"https://api.github.com/users/Pellarin","html_url":"https://github.com/Pellarin","followers_url":"https://api.github.com/users/Pellarin/followers","following_url":"https://api.github.com/users/Pellarin/following{/other_user}","gists_url":"https://api.github.com/users/Pellarin/gists{/gist_id}","starred_url":"https://api.github.com/users/Pellarin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Pellarin/subscriptions","organizations_url":"https://api.github.com/users/Pellarin/orgs","repos_url":"https://api.github.com/users/Pellarin/repos","events_url":"https://api.github.com/users/Pellarin/events{/privacy}","received_events_url":"https://api.github.com/users/Pellarin/received_events","type":"User","site_admin":false},"created_at":"2015-05-22T08:37:53Z","updated_at":"2015-05-22T08:37:53Z","body":"Well that residue should be supported in IMP in first place. These are the residues that are currently supported in IMP.atom.Residue:\r\n\r\n```\r\n\r\n//! Unknown residue\r\nIMPATOMEXPORT extern const ResidueType UNK;\r\n/** \\see ResidueType\r\n    glycine G*/\r\nIMPATOMEXPORT extern const ResidueType GLY;\r\n#ifndef IMP_DOXYGEN\r\n/* Code currently assumes that all indices between GLY.get_index()\r\n   and TRP.get_index() being amino acids */\r\n//! alanine A\r\nIMPATOMEXPORT extern const ResidueType ALA;\r\n//! valine V\r\nIMPATOMEXPORT extern const ResidueType VAL;\r\n//! leucine L\r\nIMPATOMEXPORT extern const ResidueType LEU;\r\n//! isoleucine I\r\nIMPATOMEXPORT extern const ResidueType ILE;\r\n//! serine S\r\nIMPATOMEXPORT extern const ResidueType SER;\r\n//! threonine T\r\nIMPATOMEXPORT extern const ResidueType THR;\r\n//! cysteine C\r\nIMPATOMEXPORT extern const ResidueType CYS;\r\n//! methionine M\r\nIMPATOMEXPORT extern const ResidueType MET;\r\n//! proline P\r\nIMPATOMEXPORT extern const ResidueType PRO;\r\n//! aspartic acid D\r\nIMPATOMEXPORT extern const ResidueType ASP;\r\n//! asparagine N\r\nIMPATOMEXPORT extern const ResidueType ASN;\r\n//! glutamine Q\r\nIMPATOMEXPORT extern const ResidueType GLU;\r\n//! glutamic acid E\r\nIMPATOMEXPORT extern const ResidueType GLN;\r\n//! lysine K\r\nIMPATOMEXPORT extern const ResidueType LYS;\r\n//! arginine N\r\nIMPATOMEXPORT extern const ResidueType ARG;\r\n//! histidine H\r\nIMPATOMEXPORT extern const ResidueType HIS;\r\n//! phenylalanine F\r\nIMPATOMEXPORT extern const ResidueType PHE;\r\n//! tyrosine Y\r\nIMPATOMEXPORT extern const ResidueType TYR;\r\n//! tryptophan W\r\nIMPATOMEXPORT extern const ResidueType TRP;\r\n//! ACE\r\nIMPATOMEXPORT extern const ResidueType ACE;\r\n//! end group\r\nIMPATOMEXPORT extern const ResidueType NH2;\r\n/* Code currently assumes that all indices between ADE.get_index()\r\n   and DTHY.get_index() being nucleic acid */\r\n//! adenine (RNA)\r\nIMPATOMEXPORT extern const ResidueType ADE;\r\n//! uracil (RNA)\r\nIMPATOMEXPORT extern const ResidueType URA;\r\n//! cytosine (RNA)\r\nIMPATOMEXPORT extern const ResidueType CYT;\r\n//! guanine (RNA)\r\nIMPATOMEXPORT extern const ResidueType GUA;\r\n//! thymine (RNA)\r\nIMPATOMEXPORT extern const ResidueType THY;\r\n//! adenine (DNA)\r\nIMPATOMEXPORT extern const ResidueType DADE;\r\n//! uracil (DNA)\r\nIMPATOMEXPORT extern const ResidueType DURA;\r\n//! cytosine (DNA)\r\nIMPATOMEXPORT extern const ResidueType DCYT;\r\n//! guanine (DNA)\r\nIMPATOMEXPORT extern const ResidueType DGUA;\r\n//! thymine (DNA)\r\nIMPATOMEXPORT extern const ResidueType DTHY;\r\n\r\n// All further residues (including user-added residues) are ligands\r\n\r\n//! water molecule\r\nIMPATOMEXPORT extern const ResidueType HOH;\r\n//! heme\r\nIMPATOMEXPORT extern const ResidueType HEME;\r\n#endif\r\n/*@}*/\r\n```"}}