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Timeline
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 …
Jul 8, 2016:
- 2:23 PM Ticket #363 ("view atomspec" doesn't work if only ribbons/cartoons shown) closed by
- fixed: Fixed. view command was not considering ribbons with all atoms …
- 1:26 PM Ticket #364 (map_series_gui tool not initialized) created by
- The map series gui tool was not being initialized. The initialize() …
- 11:14 AM Ticket #363 ("view atomspec" doesn't work if only ribbons/cartoons shown) created by
- I can't focus in on specific residues with the view command when only …
- 10:34 AM Ticket #362 (Report average, min, max electrostatic potential on surface) created by
- Begin forwarded message: From: "Marek Maly" Subject: Re: …
Jul 7, 2016:
- 3:00 PM DeveloperMeetings edited by
- (diff)
- 2:41 PM 2016-07-07 created by
- 2:41 PM FAI edited by
- (diff)
- 2:28 PM FAI edited by
- (diff)
- 12:34 PM Ticket #361 (hiding cartoon/ribbon for any N-terminal part of an SSE causes a problem) created by
- This may be the same problem as #333, I'm not sure. If you hide a …
- 11:12 AM Ticket #360 (cartoon tether with atomspec gives error) created by
- I can use "cartoon tether" without error if I don't specify any atoms …
Jul 6, 2016:
- 3:02 PM Ticket #359 (giving color-cmd target as a single keyword instead of with target ...) closed by
- fixed: Fixed.
- 11:48 AM Ticket #359 (giving color-cmd target as a single keyword instead of with target ...) created by
- In the current daily build, using commands like "color pink cartoon" …
Jul 5, 2016:
- 4:43 PM Ticket #358 (cannot open session just saved in same version) closed by
- fixed: Change from using gzip.GzipFile to gzip.open so that 'encoding' …
- 10:59 AM Ticket #358 (cannot open session just saved in same version) created by
- I first created the session with these commands and then some manual …
- 9:48 AM Ticket #253 (ribbon 3j3f gives error) closed by
- fixed: apparently fixed, neither 3j3f or "ribbon nucleic" on 4v6x generate …
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