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Timeline
Jun 14, 2018:
- 3:12 PM Ticket #1168 ("safe mode" startup for use with devel command) created by
- It would be useful to have a "safe mode" startup flag for Chimerax …
- 2:44 PM 2018-06-14 created by
- 2:30 PM Ticket #620 (Create initial bundle development example with documentation) closed by
- fixed: More editing will help.
- 2:07 PM DeveloperMeetings edited by
- (diff)
- 10:35 AM Ticket #1129 (ffmpeg on OSX 10.11: dyld: Symbol not found: _clock_gettime) closed by
- duplicate: Same as #983.
- 10:35 AM Ticket #983 (ffmpeg on OSX 10.11: dyld: Symbol not found: _clock_gettime) closed by
- wontfix: Fixing this requires some effort because we would have to work around …
Jun 12, 2018:
- 5:08 PM Ticket #662 (ribbon "normalization error") closed by
- fixed: Fixed in 6968fa470. Was using a vector on the assumption …
- 11:00 AM Ticket #1167 (Re:) created by
- […]
- 7:59 AM Ticket #1166 (Ribbon: operands could not be broadcast together with shapes) created by
- […] smime.p7s
- 4:10 AM Ticket #1165 (Ramachandran plot in ISOLDE (libbz2.so.1.0 not found)) created by
- […]
Jun 11, 2018:
- 2:13 PM Ticket #1162 (Execution of 'Structure' object's '_graphics_changed' property raised ...) closed by
- fixed: Doesn't happen in nogui mode. Fixed by added 'if not mol.deleted:'
Jun 8, 2018:
- 12:23 PM Ticket #1161 (undo traceback) closed by
- fixed: Fixed in 81635c182. UserError exception is thrown now, …
Jun 7, 2018:
- 4:56 PM Ticket #1160 (Issue with morphing) closed by
- fixed: "position changed" was being change-tracked on an unopened model (i.e. …
- 3:21 PM 2018-06-07 created by
- 2:10 PM DeveloperMeetings edited by
- (diff)
- 1:25 PM Ticket #1164 (port filled rings from Chimera) created by
- Filled sugar and bases rings has been requested as the default for all …
- 8:54 AM Ticket #1163 (Sample Error Tool) created by
- […] [[Image(...)]] …
Jun 6, 2018:
- 5:07 PM Ticket #1123 (PDB output not updating HELIX/SHEET) closed by
- fixed: Fix will be in the next build
- 3:58 PM Ticket #1162 (Execution of 'Structure' object's '_graphics_changed' property raised ...) created by
- The following command (must be on one line) causes nucleotides to call …
- 2:37 PM Ticket #1161 (undo traceback) created by
- Reproduce with: […] The traceback is: […] Discussion: Putting …
- 2:24 PM Ticket #949 (Tool window dragging problematic on Linux) closed by
- nonchimerax: Appears to be fixed with Qt 5.9.5.
- 12:22 PM Ticket #1155 (RFE: rounded ends on nucleotide stubs) closed by
- fixed: Fixed!
Jun 5, 2018:
- 10:03 PM Ticket #1154 (cannot use "open" command with URL) closed by
- fixed
- 5:29 PM Ticket #1159 (Issue with morphing) closed by
- duplicate: duplicate of #1160
- 5:29 PM Ticket #1158 (Issue with morphing) closed by
- duplicate: duplicate of #1160
- 5:05 PM Ticket #1160 (Issue with morphing) created by
- […]
- 5:04 PM Ticket #1159 (Issue with morphing) created by
- […]
- 5:04 PM Ticket #1158 (Issue with morphing) created by
- […]
- 4:00 PM Ticket #1157 (need to change initial display of nucleotides) created by
- The current initial display of nucleotides has the same issues I …
- 3:53 PM Ticket #1156 (RFE nucleotide color follows residue (cartoon) color instead of atom color) created by
- This is already true for ladder and stub nucleotide representations. …
- 3:48 PM Ticket #1155 (RFE: rounded ends on nucleotide stubs) created by
- Nucleotide stubs would look nicer with rounded ends.
- 3:07 PM Ticket #1103 (AddH fails after deleting atoms) closed by
- fixed: It looks like what you are importing from molobject is all the …
- 11:58 AM Ticket #1153 (surface_zone() before first drawing has no effect) closed by
- fixed: Fixed. Surface zone initially done on an empty surface was not doing …
- 11:55 AM Ticket #1154 (cannot use "open" command with URL) created by
- For example open http://www.rbvi.ucsf.edu/chimera/index.html …
- 8:47 AM Ticket #1103 (AddH fails after deleting atoms) reopened by
- This is still happening in the current 0.7 build. If I load a model …
- 8:16 AM Ticket #696 (File/save causing segmentation fault in Linux) closed by
- fixed: Just checked in the latest 0.7 build. No more crash.
- 8:15 AM Ticket #925 (Severe degradation in threaded performance on Linux) closed by
- fixed: This old ticket is well and truly obsolete now.
- 1:42 AM Ticket #1153 (surface_zone() before first drawing has no effect) created by
-
Previously it was possible to mask a volume using
surface_zone()…
Jun 4, 2018:
- 6:46 PM Ticket #1152 (open pdbdev:4 gives error) closed by
- fixed: Fixed. This IHM model had missing model group names. Added code to …
- 5:00 PM Ticket #1152 (open pdbdev:4 gives error) created by
- UCSF ChimeraX version: 0.7 (2018-06-03) open pdbdev:4 Summary of …
- 11:14 AM Ticket #1151 (pausing cursor over nucleotide ladder or stubs causes tracebacks) closed by
- fixed: Fixed. In some case Nucleotides was passing in the residue as the …
- 10:23 AM Ticket #1151 (pausing cursor over nucleotide ladder or stubs causes tracebacks) created by
- UCSF ChimeraX version: 0.7 (2018-06-03) open 1bna nuc stubs ... move …
- 10:08 AM 2018-05-31 edited by
- (diff)
Jun 2, 2018:
- 4:45 PM Ticket #1150 (Off-line documentation search capability) created by
- It would be nice if we can search documentation that comes with …
- 4:41 PM Ticket #838 (Name selection command/GUI) closed by
- fixed: Completed.
- 4:40 PM Ticket #1067 (Automatically extend registration when using toolshed) closed by
- fixed: Completed. Currently, no statistics are being captured about …
Jun 1, 2018:
- 4:24 PM Ticket #1128 (Proxy server support) closed by
- fixed: Hi Vincent, I have added HTTP/HTTPS proxy server support and I'm …
May 31, 2018:
- 2:50 PM 2018-05-31 created by
- 2:04 PM DeveloperMeetings edited by
- (diff)
- 1:33 PM Ticket #1149 (bundles need test suites) created by
- This ticket addresses pre-release testing, that is testing that is …
- 11:09 AM Ticket #1145 (Assign B-factors to added atoms) closed by
- fixed: Swapaa mouse mode now sets the side chain b-factors of the new residue …
- 10:42 AM Ticket #1148 (Repeat calls to 'cofr showpivot true' sheds pivot indicator colors) closed by
- fixed: Fixed.
- 7:00 AM Ticket #1148 (Repeat calls to 'cofr showpivot true' sheds pivot indicator colors) created by
-
If the pivot indicator is already showing, then
cofr showpivot true… - 3:26 AM Ticket #1147 (make failing when bundle has a pip dependency) created by
- Finally getting around to updating to version 0.7, and building the …
May 30, 2018:
- 4:54 PM Ticket #1144 (Bad geometry leaves histidine HE2 unbonded on PDB load) closed by
- fixed: I wouldn't normally bother with this kind of problem since …
- 3:54 PM Ticket #1146 (Bond rotation mouse mode broken) closed by
- fixed
- 1:38 PM Ticket #783 (Integrate bundle help files with core help) closed by
- fixed
- 11:05 AM Ticket #1146 (Bond rotation mouse mode broken) created by
- Using bond rotation mouse mode gives the following error in current …
- 6:18 AM Ticket #1145 (Assign B-factors to added atoms) created by
- This applies to AddH and SwapAA at present. It would be great if the …
- 1:50 AM Ticket #1144 (Bad geometry leaves histidine HE2 unbonded on PDB load) created by
- This is a fairly artificial situation, but nonetheless... As a test …
May 29, 2018:
- 1:09 PM Ticket #1143 (Toolbar clipped on high DPI display, Windows 10) created by
- […]
- 11:48 AM Ticket #1142 (after isolde install) created by
- […]
- 11:48 AM Ticket #1141 (Unable to install clipper) created by
- […]
- 10:45 AM Ticket #1133 (3D hardware stereo not working chimeraX in RHEL7) closed by
- nonchimerax: I am not surprised by your experience. We have quad-buffered stereo …
May 25, 2018:
- 1:38 PM Ticket #1139 (File drop: name 'p' is not defined) closed by
- fixed: This bug was fixed some time ago. Please use the ChimeraX daily …
- 11:30 AM Ticket #1140 (problem with v0.6 and v0.7) created by
- […]
- 7:07 AM Ticket #1139 (File drop: name 'p' is not defined) created by
- […]
May 23, 2018:
- 11:59 AM Ticket #1138 (Add NIfTI microscopy file format reader) created by
- ConfocalVR uses the NIfTI file format. Would be helpful for ChimeraX …
- 11:58 AM Ticket #1137 (Add popup menu display in VR gui panel) created by
- Would like to be able to adjust volume step using step menu in volume …
- 11:56 AM Ticket #1136 (Allow drag on VR gui panel to adjust volume thresholds) created by
- Would like to be able to adjust grayscale image thresholds in VR by …
- 11:40 AM Ticket #1135 (Better automatic volume step for light microscopy) created by
- Most light microscopy 3d images have z voxel size 5 times larger than …
May 22, 2018:
- 3:51 PM Ticket #1134 (VR gui panel does not work hidden on desktop) created by
- If the VR gui panel on Windows 10 is iconified or another application …
- 3:51 PM Ticket #1133 (3D hardware stereo not working chimeraX in RHEL7) created by
- […]
- 3:50 PM Ticket #1132 (Opening Imaris microscopy excruciatingly slow) created by
- Opening large Imaris 3D/4D microscopy data is extremely slow. This is …
- 1:24 PM ChangeLog edited by
- (diff)
- 12:20 PM Ticket #1131 (ISOLDE not compatible with v 0.7?) created by
- […]
- 11:31 AM Ticket #1130 ("info models" gives long string instead of model number) closed by
- fixed
May 21, 2018:
- 9:41 AM Ticket #1130 ("info models" gives long string instead of model number) created by
- open 1gcn info models model id <bound method Structure.atomspec of …
May 18, 2018:
- 10:42 AM Ticket #856 (Investigate replacing ctypes in atomic with Cython) closed by
- fixed: Well, if the ticket is for "investigation", that certainly has been …
- 9:07 AM Ticket #1129 (ffmpeg on OSX 10.11: dyld: Symbol not found: _clock_gettime) created by
- […]
May 17, 2018:
- 9:59 PM Ticket #752 (CIF/PDB I/O problems) closed by
- fixed: I'm going to consider this "fixed" for now. The sheets are still a …
- 4:24 PM Ticket #1112 (Execution problem) closed by
- nonchimerax: ChimeraX is only for 64-bit versions of Windows. Check which version …
- 1:11 PM Ticket #1120 (links in Log to help pages cannot be opened) closed by
- fixed: Fixed. Need to use help: URLs for commands instead file: URLs, so …
- 12:45 PM Ticket #1125 (Functionality 'nucleotides' not working) closed by
- fixed: Fixed. "New" Drawing.set_geometry() cleared vertex_colors, which the …
- 10:56 AM Ticket #1127 (Isolde installation error) closed by
- not a bug
- 10:53 AM Ticket #1128 (Proxy server support) created by
- Need to offer proxy-server support for toolshed and other facilities …
- 10:47 AM Ticket #1105 (ISOLDE run time error) closed by
- fixed: Thank for the info Vincent! It will be helpful if or when others run …
May 16, 2018:
- 11:48 PM Ticket #1117 ('help' produces 'usage' for many commands) closed by
- fixed: Fixed. Was broken by code for supporting documentation in bundles.
- 1:57 PM Ticket #1127 (Isolde installation error) created by
- […]
- 11:00 AM Ticket #1126 (Functionality 'nucleotides' not working) closed by
- duplicate: Apparent duplicate of #1125
- 5:36 AM Ticket #1126 (Functionality 'nucleotides' not working) created by
- […] [[Image(...)]]
- 4:44 AM Ticket #1125 (Functionality 'nucleotides' not working) created by
- […] [[Image(...)]]
- 2:03 AM Ticket #1124 (Remove bot traffic from Toolshed download stats?) created by
- The Toolshed download statistics page is a really cool tool that I …
May 15, 2018:
- 2:23 PM Ticket #1123 (PDB output not updating HELIX/SHEET) created by
- As per summary
- 1:52 PM Ticket #1122 (AddH adds spurious hydrogen to dangling 5' phosphate) created by
- Analogous to a dangling N-terminus, it's reasonably common to see …
- 1:24 PM Ticket #1121 (Erroneous bonding at RNA chain break in PDB 5an9) created by
- In the current daily build, residues N2700, N2925, and N2926 are all …
- 11:26 AM Ticket #1120 (links in Log to help pages cannot be opened) created by
- for example, open some structure, use command "info models", and then …
- 2:02 AM Ticket #1119 (Misleading pseudobond at RNA chain break in mmCIF 5an9) created by
- Opening 5an9, residues N2700 and N2925 (the 3' and 5' sides of a chain …
- 1:32 AM Ticket #1118 (deleting residues from a chain leads to erroneous PDB) created by
- If I open a PDB file, select some set of residues in the middle of a …
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