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Timeline
Aug 10, 2016:
- 3:58 PM Ticket #407 (Update status line during long computations) closed by
- fixed: Fixed. Added limited event processing to the MainWindow status() …
- 3:51 PM Ticket #407 (Update status line during long computations) created by
- The Qt status line does not update with new status messages unless the …
- 2:52 PM Ticket #406 (Cartoon for C-alpha only structures) created by
- Show ribbon for C-alpha only structures, for example, 4bml.
- 12:59 PM SourceCode edited by
- (diff)
- 12:58 PM Ticket #402 (nonstandard RNA residues cause cartoon (ribbon) problems) closed by
- fixed: "Fixed" in 8786937. Added code to set non-amino-acid, …
- 12:32 PM Ticket #404 (ChimeraX fails to start if tool is missing) closed by
- fixed: Fixed in 2c1b0ad. When bootstrapping, remove from session …
- 12:11 PM Ticket #405 (Volume solid style doesn't look good along x or y axes) created by
- Begin forwarded message: Volume solid style display currently only …
- 10:05 AM Ticket #404 (ChimeraX fails to start if tool is missing) created by
- Trying to run any older version of ChimeraX fails because it does not …
Aug 9, 2016:
- 3:04 PM Ticket #403 (nonstandard RNA residues missing rungs) closed by
- fixed: Fixed. Rungs now shown for non-standard nucleic acids. The rungs …
- 12:46 PM Ticket #403 (nonstandard RNA residues missing rungs) created by
- Modified RNA residues in structures such as 1ehz are missing "rung" …
- 12:22 PM Ticket #402 (nonstandard RNA residues cause cartoon (ribbon) problems) created by
- It looks like the nonstandard nucleic acid residues in a tRNA (for …
- 11:21 AM Ticket #399 (Pressing delete key in log window goes back in html history) closed by
- fixed
- 11:18 AM Ticket #398 (Command-line loses focus when clicking toolbar button) closed by
- fixed: Fixed. I made the top level ChimeraX window forward keystrokes to the …
Aug 8, 2016:
- 3:29 PM Ticket #401 (Label sizes on 4k / retina displays) created by
- Specifying label sizes in pixels makes their initial size very …
Aug 5, 2016:
- 7:38 PM Ticket #400 (Pressing enter in volume viewer level entry causes command-line execution) closed by
- fixed: False alarm. This was caused by test code where I had ui/gui.py …
- 5:09 PM Ticket #400 (Pressing enter in volume viewer level entry causes command-line execution) created by
- Pressing the enter key while clicked into the volume viewer panel …
- 5:03 PM Ticket #399 (Pressing delete key in log window goes back in html history) created by
- Clicking into the log window (Qt) and pressing delete goes back in the …
- 4:56 PM Ticket #398 (Command-line loses focus when clicking toolbar button) created by
- In Qt, clicking any toolbar button, e.g. background color gray, makes …
Aug 4, 2016:
- 5:54 PM Ticket #383 (leftover old-color triangles in recolored surface) closed by
- fixed: Fixed. When a molecular surface changes shape it now becomes a single …
- 5:15 PM Ticket #368 (Log window in Qt version steals focus from Command Line) closed by
- fixed: Fixed by having the log remember what the active window was before it …
- 3:02 PM 2016-08-04 created by
- 2:57 PM FAI edited by
- (diff)
- 2:10 PM 2016-07-28 edited by
- (diff)
Aug 3, 2016:
- 6:48 PM Ticket #397 (Missing bonds in mmCIF 1tna) created by
- Opening 1tna mmCIF is missing many backbone bonds. (And the missing …
- 6:44 PM Ticket #394 (error saving model image) closed by
- fixed: Fixed. Initial display of 1tna.cif shows nothing and that caused …
- 6:30 PM Ticket #395 (surf enclose traceback) closed by
- fixed: Fixed. surface command with enclose option specifying 0 atoms gave …
- 4:19 PM Ticket #391 (cannot use "sides" option of command "cartoon style") closed by
- fixed: Fixed in 69737fb. The "sides" option in "cartoon style" …
- 4:00 PM Ticket #396 (cannot show Side View) created by
- starting ChimeraX daily build (Qt) and choosing menu: Tools... Side …
- 3:58 PM Ticket #392 ("round" ribbon (cartoon) normals may be wrong) closed by
- fixed: There was indeed a bug, and is fixed in 17a02c6. When an …
- 3:49 PM Ticket #395 (surf enclose traceback) created by
- If you open 1gcn, then 'surf enclose nucleic', you get the following …
- 3:05 PM Ticket #391 (cannot use "sides" option of command "cartoon style") reopened by
- Oh, I see. It only applies to the barbell xsection right now. I …
- 2:41 PM Ticket #391 (cannot use "sides" option of command "cartoon style") closed by
- fixed: Fixed in bef4ccb. There was a conflict because command …
- 2:14 PM Ticket #394 (error saving model image) created by
- When opening 1tna, I get the following traceback: […]
- 2:13 PM Ticket #390 (incorrect parsing of semicolon command separator) closed by
- fixed: Fixed.
- 12:47 PM Ticket #393 (rungs weirdness) closed by
- fixed: Fixed. Rungs command now promotes atomspec to residues, and hide …
- 11:19 AM Ticket #393 (rungs weirdness) created by
- Two possibly related and low-probability things, file as desired. (1) …
- 10:06 AM Ticket #392 ("round" ribbon (cartoon) normals may be wrong) created by
- Maybe there's a bug making the ribbons look too fat and bulgy, see …
- 10:02 AM Ticket #391 (cannot use "sides" option of command "cartoon style") created by
- "Cartoon style" usage info limits sides to 3-10 but clearly can be set …
Aug 2, 2016:
- 3:22 PM Ticket #268 (cartoon short strands not smoothed or smoothable) closed by
- fixed: Seems to be working now. I tested the command […] and it …
- 3:15 PM Ticket #387 (~cartoon/cartoon cycle does not hide backbone) closed by
- fixed: This is related to #221. It looks like the all atoms of selected …
- 2:58 PM Ticket #221 (Proline N atom floats away from ribbon) closed by
- fixed: Semi-fixed in d21172f. The bond between N and CA is now …
- 1:17 PM Ticket #177 (Ribbon end-cap shows striped marks) closed by
- fixed: Seems to be fixed. Cannot seem to find any changeset that might have …
- 12:28 PM Ticket #175 (2x slower opening 3j3q) closed by
- fixed: The _create_ribbon_graphics method now shortcuts to return quickly …
- 12:13 PM Ticket #161 (Ribbon normals are weird, 1a0m chain B) closed by
- fixed: Fixed. Could have been one of several changes made for ribbon orientation.
- 12:04 PM Ticket #141 (Chain atom spec includes density maps) closed by
- fixed: Appears to be fixed. Probably fixed by fc26ebc.
- 12:03 PM Ticket #390 (incorrect parsing of semicolon command separator) created by
- Example: open 5chz surf enclose protein; surf enclose nucleic …
- 11:34 AM Ticket #102 (Strange atom spec parsing of model ids with commas) closed by
- fixed: Fixed in e26d659. There was a copy-and-paste error where …
- 10:58 AM Ticket #348 (opening 1a0s gives traceback and no cartoons shown) closed by
- fixed: Fixed in 3af8e272. The problem is that there are residues …
- 10:55 AM Ticket #265 (cartoon (ribbon) helix inside-out problems) closed by
- fixed: The problem is "fixed". I think the issue is that the orientation of …
- 10:44 AM Ticket #174 (Chimera starts with no tools) closed by
- worksforme: Tested all three versions: looping over - unsorted entries, - sorted …
- 10:31 AM Ticket #182 (loooong tethers) closed by
- fixed: There is no tether displayed for /v:107 in 1www in the latest build, …
Aug 1, 2016:
- 5:28 PM Ticket #386 (Session saving from dialog fails) closed by
- fixed: Fixed.
- 5:26 PM Ticket #389 (Session save slow for molecular surfaces) created by
- Takes 10 seconds to save a session with 4hhb with molecular surfaces …
- 4:06 PM Ticket #388 (surface doesn't notice when some of its atoms are deleted) created by
- for example open 2gbp surf color :lys yellow targ as delete :lys ... …
- 3:10 PM Ticket #382 (cannot use "format" keyword with "save") closed by
- fixed: Fixed save command format option. Fixed "usage map save" so it lists …
- 11:50 AM Ticket #387 (~cartoon/cartoon cycle does not hide backbone) created by
- If I hide and re-show cartoon, the mainchain atoms are still shown. …
Jul 29, 2016:
- 10:36 AM Ticket #386 (Session saving from dialog fails) created by
- Traceback (most recent call last): File …
Jul 28, 2016:
- 2:45 PM DeveloperMeetings edited by
- (diff)
- 2:44 PM 2016-07-28 created by
- 2:10 PM FAI edited by
- (diff)
Jul 27, 2016:
- 2:00 PM Ticket #385 (problems with atomspec "nucleic acid") closed by
- invalid: Oops got confused between Chimera and ChimeraX. In the latter it is …
- 1:49 PM Ticket #385 (problems with atomspec "nucleic acid") created by
- I am sure atomspec "nucleic acid" worked at some point, but currently …
Jul 25, 2016:
- 5:31 PM Ticket #384 (problem dealing with microheterogeneity) created by
- Open 1ejg or 1cbn in mmcif or pdb format, and then "turn y 90" and you …
- 4:13 PM Ticket #383 (leftover old-color triangles in recolored surface) created by
- This is a bit circuitous, but if I do this open 2gbp surf color tan …
- 11:32 AM Ticket #382 (cannot use "format" keyword with "save") created by
- Using UCSF ChimeraX version: 0.1 (2016-07-22) command: save #3 …
Jul 21, 2016:
- 3:10 PM 2016-07-21 edited by
- (diff)
- 3:01 PM 2016-07-21 created by
- 2:02 PM DeveloperMeetings edited by
- (diff)
- 1:33 PM Ticket #360 (cartoon tether with atomspec gives error) closed by
- fixed: Fixed in 47505c4/chimerax. The command parsing code was …
- 10:22 AM Ticket #381 (ribbons failure prevents usage) closed by
- fixed: Fixed in 1a5e477/chimerax. Use coil-coil cross sections …
- 9:55 AM Ticket #379 (cartoon linker problems with contiguous helices) closed by
- fixed: Fixed in 0281404/chimerax to not use same variable name …
- 1:06 AM Ticket #381 (ribbons failure prevents usage) created by
- Try opening 1ejg or 1cbn, both give error popups with RuntimeErrors -- …
Jul 20, 2016:
- 4:14 PM Ticket #380 (Improve atom categorization) created by
- In 5chz, the two shorter DNA strands base-paired with the longer …
- 4:02 PM Ticket #379 (cartoon linker problems with contiguous helices) created by
- PDB 5CHZ protein chain A has some contiguous helices: HELIX 5 AA5 ASP …
- 3:51 PM Ticket #378 (Atom spec parsing stops at non-whitespace) created by
- Atom spec parsing is terminating at a non-whitespace character. For …
- 2:42 PM Ticket #377 (cartoon tether can't take modelspec or atomspec) closed by
- duplicate: oops, duplicate of #360
- 12:15 PM Ticket #377 (cartoon tether can't take modelspec or atomspec) created by
- Currently I can use "cartoon tether" with a blank spec only. Using any …
Jul 19, 2016:
- 5:48 PM Ticket #83 (Importing PyTables HDF5 wrapper generates BytesWarning) closed by
- fixed: Took out our debug code that enabled BytesWarning.
- 5:47 PM Ticket #149 (wx atomspec balloon focus bugs, mac) closed by
- wontfix: Switching to Qt toolkit.
- 5:45 PM Ticket #290 (can't select dashed lines) closed by
- fixed: Working in my tests.
- 5:42 PM Ticket #369 (Volume Viewer : opening new volume changes graphics window size) closed by
- wontfix: If the docked tool panels don't fit they will cause the main window to …
- 5:40 PM Ticket #336 (2x scaling errors with Mac retina display) closed by
- fixed: Fixed. Added pixel scale parameter which is 2 for retina and 1 for …
- 5:38 PM Ticket #375 (Help viewer in Qt version does not log use of execution links) closed by
- fixed: Fixed.
Jul 18, 2016:
- 7:41 PM Ticket #376 (volume viewer close/open errrors) closed by
- fixed: Fixed.
- 4:11 PM Ticket #376 (volume viewer close/open errrors) created by
- Closing all volume data does not collapse or close Volume Viewer, …
- 2:30 PM Ticket #375 (Help viewer in Qt version does not log use of execution links) created by
- Clicking a link in the Help viewer to execute a command does execute …
- 2:26 PM Ticket #373 (clicking spin-movie icon gives tracebacks) closed by
- fixed: Fixed. Someone changed movie code putting in some tabs causing …
- 2:09 PM Ticket #374 (Help viewer in Qt version does not show movie) created by
- The Help viewer in the wx version of ChimeraX shows the movie in the …
- 2:03 PM Ticket #373 (clicking spin-movie icon gives tracebacks) created by
- I was running through the Quick Start to doublecheck the last set of …
Jul 15, 2016:
- 2:37 PM Ticket #372 (Search in help viewer gives error) closed by
- fixed: Unlike QWebPage, QWebEnginePage automatically does wrap-around search …
- 11:46 AM Ticket #371 (File history links give an error after a session restore) closed by
- fixed: Fixed. QWebEngineView link dispatching for unrecognized schema's is …
Jul 14, 2016:
- 7:03 PM Ticket #372 (Search in help viewer gives error) created by
- Typing anything in the help viewer search box and pressing return …
- 6:57 PM Ticket #371 (File history links give an error after a session restore) created by
- After restoring a session, all links in the file history tool are …
- 5:32 PM Ticket #351 (Turning on soft/full lighting hides a surface within a transparent surface) closed by
- fixed: I decided a better solution is if the transparent surface casts no …
- 3:52 PM Ticket #370 (cannot go Back after going to external web pages) created by
- In the Qt version but not the Wx version, clicking a link to an …
- 3:37 PM Ticket #369 (Volume Viewer : opening new volume changes graphics window size) created by
- Maybe only I will experience this, due to my tiny window …
- 3:29 PM Ticket #368 (Log window in Qt version steals focus from Command Line) created by
- In the Qt version but not the Wx version, if I have the Log as a …
- 3:07 PM 2016-07-14 edited by
- (diff)
- 3:04 PM DeveloperMeetings edited by
- (diff)
- 2:34 PM 2016-07-14 created by
Jul 13, 2016:
- 2:27 PM Ticket #69 (Atom spec parsing does not preserve model or chain order) reopened by
- Only the case of a spec like #1 #2 #3 was fixed 4 months ago giving …
Jul 12, 2016:
- 7:31 PM Ticket #367 (Error after deleting all atoms) created by
- Deleting all atoms causes the C++ code to delete the AtomicStructure, …
- 3:42 PM Ticket #366 (incomplete logging from multi-command cxcmd links) created by
- I guess this linking technology will change, but when it does, make …
- 12:49 PM Ticket #333 (SSE cartoon extensions toward Nterm (no preceding linker) disjoint) closed by
- fixed: #361 has been fixed.
- 12:48 PM Ticket #361 (hiding cartoon/ribbon for any N-terminal part of an SSE causes a problem) closed by
- fixed: Fixed in d91c2c5/chimerax. Twist in ribbon are ignored at …
- 10:28 AM Ticket #365 (cartoon linker error) closed by
- fixed: Fixed in 07fd9cb/ChimeraX. _RIBBON_CHANGE constant is …
Jul 11, 2016:
- 3:39 PM Ticket #364 (map_series_gui tool not initialized) closed by
- worksforme: Unable to reproduce the bug. The initialize function is being called. …
- 2:57 PM Ticket #266 (CA-only structure not using pseudobonds) closed by
- fixed
- 11:40 AM Ticket #365 (cartoon linker error) created by
- open 2gbp carlink long s,h gives traceback: cartoon linker long …
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