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4:46 PM Ticket #436 (Tool setup.py cannot register multiple extensions for file format) created by Eric Pettersen: FASTA and several other sequence formats have no "standard" file …

4:47 PM Ticket #435 (strand command-line selector broken) closed by Eric Pettersen: fixed: Fixed. Conrad missed the 'strand' and 'coil' selectors when he …
4:40 PM Ticket #435 (strand command-line selector broken) created by Elaine Meng: trying to use atomspec "strand" gives error (e.g. "sel strand") …
4:32 PM 2016-09-22 edited by Elaine Meng: (diff)
4:30 PM DeveloperMeetings edited by Conrad Huang: (diff)
4:09 PM 2016-09-22 created by Conrad Huang

2:52 PM Ticket #434 ("ts refresh" gives traceback mentioning ihm) created by Elaine Meng: UCSF ChimeraX version: 0.1 (2016-09-16) toolshed refresh Traceback …
2:35 PM Ticket #432 (capping residue ACE considered ligand, not surfaced) closed by Eric Pettersen: fixed: Capping groups now included in polymer chain.
10:23 AM Ticket #433 (consider PISA fetch for assemblies and/or interface statistics) created by Elaine Meng: Forming URLs to retrieve data from PDBePISA: …

4:16 PM 2016-08-29 edited by Tom Ferrin: (diff)
3:32 PM Ticket #432 (capping residue ACE considered ligand, not surfaced) created by Elaine Meng: Example is both chains in 1hzx. Probably the same issue with NME …
2:54 PM 2016-09-19 created by Tom Ferrin
1:56 PM DeveloperMeetings edited by Tom Ferrin: (diff)

12:48 PM Ticket #431 (Error opening PDB with blank chain id) closed by Eric Pettersen: fixed
12:32 PM Ticket #431 (Error opening PDB with blank chain id) created by Tom Goddard: open input_nowater.pdb Summary of problems opening input_nowater.pdb: …
11:54 AM Ticket #425 (saving session changes ACE residue from chain A to chain B) closed by Eric Pettersen: fixed: The multi-atom deletion code wasn't updating chains as residues got deleted

5:33 PM Ticket #430 (buriedarea and sasa should exclude ions, solvent, ligands) created by Tom Goddard: Should the buriedarea and sasa (solvent accessible surface area) …
5:24 PM Ticket #429 (matchmaker doesn't recognize tRNA as Nucleic?) closed by Eric Pettersen: fixed: Fixed. The wrapping for the C++ function that converts 3-character …
5:23 PM Ticket #428 (buriedarea "select" should clear previous selection) closed by Tom Goddard: fixed: Ok, I made the buriedarea command "select" option replace the selection.
4:07 PM 2016-09-15 created by Conrad Huang
2:09 PM FAI edited by Conrad Huang: (diff)
2:07 PM DeveloperMeetings edited by Conrad Huang: (diff)
12:43 PM Ticket #429 (matchmaker doesn't recognize tRNA as Nucleic?) created by Elaine Meng: open 2tra open 4tra mm #1 to #2 matrix Nucleic ... gives error …
12:16 PM Ticket #428 (buriedarea "select" should clear previous selection) created by Elaine Meng: Using the "select" option of "buriedarea" with gradually increasing …

12:26 AM Ticket #426 (Drag selection is selecting more than atoms in rectangle) closed by Tom Goddard: fixed: Fixed. Planar bounds of selection frustum were assuming perspective …

2:03 PM Ticket #422 (Fails to start on Mac with spaces in install path) closed by Conrad Huang: wontfix: It's actually the comma that causes this error. Whitespace in the …
1:16 PM Ticket #427 (Add multitouch trackpad rotation and translation) created by olibclarke@…: Begin forwarded message: From: Oliver Clarke Subject: Re: show/hide …
1:14 PM Ticket #426 (Drag selection is selecting more than atoms in rectangle) created by olibclarke@…: This may be only on retina display. Begin forwarded message: From: …

7:40 AM Ticket #425 (saving session changes ACE residue from chain A to chain B) created by Elaine Meng: I opened 1hzx, deleted chain B, focused on :ace. Mousing over it …

1:45 PM Ticket #424 (mmCIF chain names) created by Eric Pettersen: Need the pdbx_poly_seq_scheme records extruded into the structure …
11:17 AM Ticket #423 (Shell error messages at startup) created by Tom Goddard: Starting Sept 9, 2016 ChimeraX daily build from a terminal spews …
10:59 AM Ticket #422 (Fails to start on Mac with spaces in install path) created by Tom Goddard: If there is a space in the path to the ChimeraX install location or in …

5:17 PM Ticket #421 (align not producing same result as Chimera 1) closed by Tom Goddard: worksforme: Eric reports that the problem is that the mmcif and pdb format …
5:01 PM Ticket #421 (align not producing same result as Chimera 1) created by Eric Pettersen: If you open 1b17 and 1ben (in that order) and then use this command: …
4:30 PM Ticket #396 (cannot show Side View) closed by Greg Couch: fixed: Sideview has been ported to Qt, so it is effectively bug-for-bug …
3:01 PM Ticket #184 (seg vault deleting atoms) closed by Greg Couch: worksforme: Lost test program :-( But haven't had any problems recently.
2:57 PM Ticket #109 (Wx defects on Linux) closed by Greg Couch: wontfix: We're not using wx anymore.
2:56 PM Ticket #366 (incomplete logging from multi-command cxcmd links) closed by Greg Couch: fixed: Not sure when this was fixed, but it works now.
10:40 AM Ticket #420 (Human readable atom specifiers) created by tic20@…: Tristan suggests allowing human-readable atom specifiers. The user …

2:24 PM Ticket #419 (Read MTZ files, compute and display real-space density) created by ajm201@…: Begin forwarded message: From: Airlie McCoy <> Subject: Re: …
11:53 AM Ticket #418 (problems with help command new-viewer option) created by Elaine Meng: Would be better to change the “help” option “new_viewer” to avoid …
11:38 AM Ticket #417 (Help viewer suggestions) created by Elaine Meng: In addition to bugs #370 and #374, here are some things that could …
11:30 AM Ticket #416 (Interactively extend xray maps to zone around atom.) created by ajm201@…: Begin forwarded message: From: Airlie McCoy Subject: [chimera-dev] …

11:01 AM Ticket #415 (Model panel expands all hierarchy when models opened/closed) created by Tom Goddard: Model panel "expands all" when models opened/closed. Have it remember …

7:04 PM Ticket #414 (PDB 5c1m: cannot find consistent set of bond orders) created by Tom Goddard: open 5c1m Summary of problems opening 5c1m fetched from pdb: …

3:47 PM Ticket #413 (ChimeraX Help menu on Mac includes Search but misleading) created by Elaine Meng: On Mac, the ChimeraX Help menu includes a "Search" that apparently …

11:33 AM Ticket #412 (Fails to start on Mac with comma in app name) created by Tom Goddard: ChimeraX fails to start if there is a comma in the app name. I had …
11:08 AM Ticket #411 (Copyright messes up Mac installer html) created by Tom Goddard: Running the Mac installer shows HTML introduction panel as raw HTML …

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