{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/ensembler/issues/35","labels_url":"https://api.github.com/repos/choderalab/ensembler/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/ensembler/issues/35/comments","events_url":"https://api.github.com/repos/choderalab/ensembler/issues/35/events","html_url":"https://github.com/choderalab/ensembler/issues/35","id":100138370,"number":35,"title":"Add an option to specify (or \"pin\") the protonation states / variants of specified residues","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-08-10T18:41:16Z","updated_at":"2015-08-12T23:03:55Z","closed_at":null,"body":"@sonyahanson would like to select the protonation states of some residues (such as the DFG Asp in kinases).\r\n\r\nCurrently, the code uses [the highest sequence identity PDB file `model.pdb.gz`](https://github.com/choderalab/ensembler/blob/master/ensembler/refinement.py#L369-L374) to [extract reference residue variants](https://github.com/choderalab/ensembler/blob/master/ensembler/refinement.py#L202-L213) that are used to assign the protonation state variants of all residues in all models.\r\n\r\nTo manually make alterations, this would mean editing the `model.pdb.gz` of the highest sequence identity model(s) manually after the modelling stage in order to change residue names appropriately (e.g. change `ASP` to `ASH` to select the protonated aspartic acid).  \r\n\r\nIn future, it would be useful to allow these alterations to be specified either via the command-line or a YAML file or something."},"comment":{"url":"https://api.github.com/repos/choderalab/ensembler/issues/comments/130472784","html_url":"https://github.com/choderalab/ensembler/issues/35#issuecomment-130472784","issue_url":"https://api.github.com/repos/choderalab/ensembler/issues/35","id":130472784,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"created_at":"2015-08-12T23:03:55Z","updated_at":"2015-08-12T23:03:55Z","body":"How are nonstandard sequences specified now? FASTA file? Is there some provision for numbering in those?  Or must they be zero indexed?"}}