![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Feb 19, 2016:
- 12:16 AM Ticket #291 (mmCIF bad _struct_conn table written by CCP4) closed by
- fixed: Log warning saying table was skipped, instead of failing.
Feb 18, 2016:
- 5:17 PM Ticket #291 (mmCIF bad _struct_conn table written by CCP4) created by
- Oliver Clarke provided the attached mmCIF file written by CCP4 which …
- 3:25 PM 2016-02-18 edited by
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- 2:41 PM 2016-02-18 edited by
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- 2:24 PM 2016-02-18 edited by
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- 2:09 PM 2016-02-18 edited by
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- 2:07 PM 2016-02-18 edited by
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- 2:06 PM 2016-02-18 created by
- 2:06 PM DeveloperMeetings edited by
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- 12:43 PM Ticket #290 (can't select dashed lines) created by
- Open 134d, neither the hydrogen bonds nor the missing structure bonds …
- 11:04 AM Ticket #289 (make "usage" more useful for internal aliases) created by
- I noticed that “usage” isn’t very useful for aliases, e.g. “usage ts” …
- 9:44 AM Ticket #288 (Circle plots to show pairwise quantities for domains, chains, ...) created by
- Begin forwarded message: From: Oliver Clarke Subject: ChimeraX …
- 9:26 AM Ticket #279 (Hiding ribbons does not redisplay hidden backbone atoms) closed by
- fixed: Actually it's the bonds that do not get restored. Should be fixed now.
Feb 17, 2016:
- 1:26 PM Ticket #284 (handle mmCIF with missing sequence information) reopened by
- I've attached another mmCIF file copy_1.cif from Oliver Clarke, this …
Feb 16, 2016:
- 4:25 PM Ticket #284 (handle mmCIF with missing sequence information) closed by
- wontfix: So this bug report was good in that support for mmCIF files with an …
- 4:03 PM Ticket #287 (Image save shortcut, use different file names) created by
- Make icon that saves image use a different image file name each time …
- 2:20 PM Ticket #286 (Difference maps with local fitting) created by
- Begin forwarded message: From: Oliver Clarke Subject: Re: ChimeraX …
- 2:18 PM Ticket #285 (Optimize map grid size based on fit of atomic model) created by
- Begin forwarded message: From: Oliver Clarke Subject: ChimeraX …
- 12:33 PM Ticket #284 (handle mmCIF with missing sequence information) created by
- mmCIF file in #278 is missing the entity_poly_seq table, so the code …
- 12:30 PM Ticket #278 (Leading spaces in atom names from mmCIF file) closed by
- fixed: Added code to strip leading and trailing spaces.
- 12:18 PM Ticket #283 (Curved helix tubes) created by
- Begin forwarded message: From: Oliver Clarke Subject: Possible …
- 12:15 PM Ticket #282 (Ribbon style editor, scaling and helix/coil/strand cross-sections) created by
- Begin forwarded message: From: Oliver Clarke Subject: Possible …
- 12:09 PM Ticket #281 (Merge command-line and Python shell) created by
- Allow typed Python code in the command-line and/or allow typed …
- 12:01 PM Ticket #280 (Show density map only near center of view, like Coot) created by
- Oliver asks for map display only near center of view, the typical Coot …
- 11:43 AM Ticket #277 (Collating log repeats collation messages loading mmCIF) closed by
- fixed: Missed one of the self._sim_info -> sim_info changes.
- 10:41 AM Ticket #279 (Hiding ribbons does not redisplay hidden backbone atoms) created by
- open 1b35 show ~cartoon All the residues are shown disconnected with …
- 10:11 AM Ticket #278 (Leading spaces in atom names from mmCIF file) created by
- The attached mmCIF file (produced by Coot) does not connect any of the …
- 10:05 AM Ticket #277 (Collating log repeats collation messages loading mmCIF) created by
- Loading an mmcif file repeats the same message "27 messages similar to …
Feb 12, 2016:
- 11:27 AM Ticket #275 (mmCIF reader can produce NaN atom coords with no error) closed by
- fixed: Warn about and skip atoms with unspecified coordinates in mmCIF files.
- 11:09 AM Ticket #276 (Can't read mmCIF with lowercase cartn_x field name) closed by
- fixed: Modified readcif code to treat category tags as case insensitive.
- 10:06 AM Ticket #276 (Can't read mmCIF with lowercase cartn_x field name) created by
- I got an mmcif file written by Coot that used _atom_site.cartn_x as a …
Feb 11, 2016:
- 7:26 PM Ticket #275 (mmCIF reader can produce NaN atom coords with no error) created by
- If an mmCIF model has ? for _atom_site.Cartn_x values then the reader …
- 3:32 PM 2016-02-11 edited by
- (diff)
- 2:54 PM 2016-02-11 edited by
- (diff)
- 1:33 PM DeveloperMeetings edited by
- (diff)
- 1:32 PM 2016-02-11 created by
- 11:49 AM 2016-02-04 edited by
- (diff)
Feb 10, 2016:
- 11:58 AM Ticket #274 (Select through transparent surface or mesh) created by
- Begin forwarded message: From: Oliver Clarke Subject: …
- 11:57 AM Ticket #273 (Update atom spec balloon immediately if modifier key held down) created by
- Begin forwarded message: From: Oliver Clarke <> Subject: …
Feb 8, 2016:
- 2:55 PM Ticket #269 (running of stack deleting bonds) closed by
- fixed: Fixed
- 2:54 PM Ticket #270 (atom in_chain false after session restore) closed by
- fixed: Wasn't setting the residue pointer to the chain as the chain was restored
Feb 5, 2016:
- 2:18 PM Ticket #272 (No help if command only has subcommands) created by
- Using the help command on a command which only has subcommands, like …
- 2:15 PM Ticket #271 (Closing tabbed wx panel crashes, Mac) created by
- Closing a tabbed wx panel using its title-bar close button crashes the …
Feb 4, 2016:
- 7:19 PM Ticket #270 (atom in_chain false after session restore) created by
- If I save a molecule in a session, then restore the session, …
- 6:05 PM 2016-02-04 edited by
- (diff)
- 4:47 PM Ticket #269 (running of stack deleting bonds) created by
- "open 101d format pdb" causes ChimeraX to segfault. Using gdb, the …
- 4:15 PM Ticket #268 (cartoon short strands not smoothed or smoothable) created by
- Cartoon of short strands is not smoothed regardless of "adjust" …
- 3:11 PM DeveloperMeetings edited by
- (diff)
- 3:11 PM 2016-02-04 created by
Feb 2, 2016:
- 2:04 PM Ticket #267 (Mistaken "bound ligand" in 1fav) created by
- In 1fav, residues 123 and 124 are being treated as bound ligand when …
Feb 1, 2016:
- 6:21 PM Ticket #266 (CA-only structure not using pseudobonds) created by
- 1gbp Should be connecting the CAs with missing-structure pseudobonds, …
- 4:51 PM Ticket #220 (every time I restore session (STL-only) it adds another Model Panel) closed by
- fixed
- 4:48 PM Ticket #260 (nogui mode on Mac gives black text on black background) closed by
- fixed: Explicitly set foreground (text) color instead of using default.
- 4:18 PM Ticket #263 (Traceback opening unknown pdb id code) closed by
- fixed: Added code to see if returned mmCIF data from PDB URL is actually a …
- 2:18 PM Ticket #265 (cartoon (ribbon) helix inside-out problems) created by
- In the current ChimeraX it is fairly common to see places where the …
- 12:10 PM Ticket #264 (Atoms permanently hidden by ribbon) created by
- Showing ribbons then deleting all but CA atoms, then hiding ribbons, …
- 12:05 PM Ticket #263 (Traceback opening unknown pdb id code) created by
- Opening a pdb id code that doesn't exist should give a simple error …
Jan 28, 2016:
- 6:53 PM Ticket #258 (No gui mode broken on mac) closed by
- fixed: Fixed. Made Lighting parameter exist even when Renderer does not.
- 6:37 PM Ticket #38 (Fix Hydra Mac install target prereq version numbers) closed by
- wontfix: Hydra retired.
- 6:37 PM Ticket #112 (Graphics crash on Mac, large surfaces) closed by
- worksforme: Crash report does not say what machine this graphics driver crash was …
- 6:28 PM Ticket #1 (Port BLAST web service to Hydra) closed by
- wontfix: Hydra no longer developed.
- 6:26 PM Ticket #134 (Smoother solvent excluded surface atom boundaries) closed by
- fixed: Done some months ago. Looks beautiful. Iteratively subdivides triangles.
- 6:23 PM Ticket #7 (Can't type spaces in Hydra command-line) closed by
- wontfix: Hydra project retired.
- 6:22 PM Ticket #45 (Make half bond coloring work per-bond) closed by
- fixed: Done some months ago.
- 6:17 PM Ticket #262 (Open 1m4x displays nothing, ribbon vertices are NaN) created by
- open 1m4x displays nothing. The "info" command shows the bounding …
- 6:16 PM Ticket #261 (ribbon hide gives error) closed by
- fixed: Alias invocation needs to save Command object to allow for underlying …
- 6:08 PM Ticket #122 (Shortcut to select all text in Log) closed by
- fixed: Add "Select All" to context menu.
- 6:04 PM Ticket #261 (ribbon hide gives error) created by
- open 1a0m ribbon hide Traceback (most recent call last): File …
- 5:52 PM Ticket #241 (HTML new-tab links do nothing in ChimeraX viewer) closed by
- fixed: <a> tags with target="_blank" are now opened in an external web browser.
- 5:50 PM Ticket #245 (External links in Quick Start Guide do nothing) closed by
- fixed: Bug was due to the <a> tags having target="_blank", so a new …
- 5:48 PM Ticket #257 (sym 2f43 gives traceback) closed by
- fixed: Fixed. 2f43 had some matrices applied to one set of chains, and …
- 5:09 PM Ticket #256 ("color seq" ignores "halfbond true"?) closed by
- fixed: Fixed. The color command halfbond option was being ignored if the …
- 4:55 PM Ticket #260 (nogui mode on Mac gives black text on black background) created by
- Text in nogui mode is unreadable on Mac OS 10.10 in a terminal with …
- 4:44 PM Ticket #259 (Tools should not save in sessions by default) created by
- Elaine points out that the contacts tool restores in sessions …
- 4:41 PM Ticket #258 (No gui mode broken on mac) created by
- cx --nogui Offscreen rendering not available 0.00% done: Initializing …
- 3:01 PM Ticket #240 (Rainbow command: Missing required "objects" positional argument) closed by
- fixed: Fixed by continuing to parse required positional arguments with an …
- 2:41 PM DeveloperMeetings edited by
- (diff)
- 2:40 PM 2016-01-28 created by
- 1:55 PM Ticket #257 (sym 2f43 gives traceback) created by
- open 2f43 sym #1 ... reports assembly 1: Assemblies for 2f43: 1 = …
- 1:11 PM Ticket #256 ("color seq" ignores "halfbond true"?) created by
- open 2gbp color cyan targ b half f rainbow res targ a half true style …
- 12:46 PM Ticket #255 (command logging messed up) closed by
- fixed: Fixed.
- 11:02 AM Ticket #246 (Commands separated by ";" are parsed before any are run) closed by
- fixed: Fixed. Changes affected error reporting.
- 9:34 AM Ticket #255 (command logging messed up) created by
- In today's build the logged commands all have 5 characters right after …
Jan 26, 2016:
- 7:03 PM PseudoBonds created by
- 7:01 PM WikiStart edited by
- (diff)
- 1:09 PM WikiStart edited by
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- 1:03 PM WikiStart edited by
- (diff)
Jan 25, 2016:
- 5:01 PM Ticket #254 (Crash deleting global pseudobond group) created by
- open 1bna open 1bna.pb (file attached) close crashes in …
- 12:03 PM GrantAims edited by
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- 12:00 PM GrantAims edited by
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- 12:00 PM GrantAims edited by
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- 11:59 AM GrantAims created by
- 11:52 AM WikiStart edited by
- (diff)
- 10:35 AM Ticket #253 (ribbon 3j3f gives error) created by
- Opening rna structure 3j3f gives an error apparently related to ribbon …
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