Timeline



Jun 22, 2018:

3:51 PM Ticket #476 (Command history dialog appears at startup) closed by pett
fixed: Fixed by commit 7335861ebf893e47a43d3b8bf7e96f3c22be7e53 in March of 2017
10:28 AM Ticket #1167 (Re:) closed by pett
invalid
10:26 AM Ticket #1171 ("ChimeraX --cmd" doesn't recognise multi-word commands) closed by pett
worksforme: Hi Tristan, You have to put quotes around a multi-word command. --Eric
2:49 AM Ticket #1171 ("ChimeraX --cmd" doesn't recognise multi-word commands) created by Tristan Croll
Enough said, really. As far as I can tell from trying every …

Jun 21, 2018:

4:07 PM 2018-06-14 edited by pett
(diff)
6:15 AM Ticket #1169 ('new frame' trigger should still fire when no models open) created by Tristan Croll
At the moment, unless I'm missing something there is no session …

Jun 14, 2018:

3:12 PM Ticket #1168 ("safe mode" startup for use with devel command) created by pett
It would be useful to have a "safe mode" startup flag for Chimerax …
2:44 PM 2018-06-14 created by Conrad Huang
2:30 PM Ticket #620 (Create initial bundle development example with documentation) closed by Conrad Huang
fixed: More editing will help.
2:07 PM DeveloperMeetings edited by Conrad Huang
(diff)
10:35 AM Ticket #1129 (ffmpeg on OSX 10.11: dyld: Symbol not found: _clock_gettime) closed by Conrad Huang
duplicate: Same as #983.
10:35 AM Ticket #983 (ffmpeg on OSX 10.11: dyld: Symbol not found: _clock_gettime) closed by Conrad Huang
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 Conrad Huang
fixed: Fixed in 6968fa470. Was using a vector on the assumption …
11:00 AM Ticket #1167 (Re:) created by Conrad Huang
[…]
7:59 AM Ticket #1166 (Ribbon: operands could not be broadcast together with shapes) created by turmand@…
[…] smime.p7s​
4:10 AM Ticket #1165 (Ramachandran plot in ISOLDE (libbz2.so.1.0 not found)) created by luigi@…
[…]

Jun 11, 2018:

2:13 PM Ticket #1162 (Execution of 'Structure' object's '_graphics_changed' property raised ...) closed by Greg Couch
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 Conrad Huang
fixed: Fixed in 81635c182. UserError exception is thrown now, …

Jun 7, 2018:

4:56 PM Ticket #1160 (Issue with morphing) closed by pett
fixed: "position changed" was being change-tracked on an unopened model (i.e. …
3:21 PM 2018-06-07 created by Conrad Huang
2:10 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:25 PM Ticket #1164 (port filled rings from Chimera) created by Greg Couch
Filled sugar and bases rings has been requested as the default for all …
8:54 AM Ticket #1163 (Sample Error Tool) created by msaqib_2020@…
[…] [[Image(...)]] …

Jun 6, 2018:

5:07 PM Ticket #1123 (PDB output not updating HELIX/SHEET) closed by pett
fixed: Fix will be in the next build
3:58 PM Ticket #1162 (Execution of 'Structure' object's '_graphics_changed' property raised ...) created by Tom Goddard
The following command (must be on one line) causes nucleotides to call …
2:37 PM Ticket #1161 (undo traceback) created by Greg Couch
Reproduce with: […] The traceback is: […] Discussion: Putting …
2:24 PM Ticket #949 (Tool window dragging problematic on Linux) closed by Greg Couch
nonchimerax: Appears to be fixed with Qt 5.9.5.
12:22 PM Ticket #1155 (RFE: rounded ends on nucleotide stubs) closed by Greg Couch
fixed: Fixed!

Jun 5, 2018:

10:03 PM Ticket #1154 (cannot use "open" command with URL) closed by Greg Couch
fixed
5:29 PM Ticket #1159 (Issue with morphing) closed by pett
duplicate: duplicate of #1160
5:29 PM Ticket #1158 (Issue with morphing) closed by pett
duplicate: duplicate of #1160
5:05 PM Ticket #1160 (Issue with morphing) created by coleman.martin@…
[…]
5:04 PM Ticket #1159 (Issue with morphing) created by coleman.martin@…
[…]
5:04 PM Ticket #1158 (Issue with morphing) created by coleman.martin@…
[…]
4:00 PM Ticket #1157 (need to change initial display of nucleotides) created by Elaine Meng
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 Elaine Meng
This is already true for ladder and stub nucleotide representations. …
3:48 PM Ticket #1155 (RFE: rounded ends on nucleotide stubs) created by Elaine Meng
Nucleotide stubs would look nicer with rounded ends.
3:07 PM Ticket #1103 (AddH fails after deleting atoms) closed by pett
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 Tom Goddard
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 Elaine Meng
For example open ​http://www.rbvi.ucsf.edu/chimera/index.html …
8:47 AM Ticket #1103 (AddH fails after deleting atoms) reopened by Tristan Croll
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 Tristan Croll
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 Tristan Croll
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 Tristan Croll
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 Tom Goddard
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 Elaine Meng
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 pett
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 Elaine Meng
UCSF ChimeraX version: 0.7 (2018-06-03) open 1bna nuc stubs ... move …
10:08 AM 2018-05-31 edited by Conrad Huang
(diff)

Jun 2, 2018:

4:45 PM Ticket #1150 (Off-line documentation search capability) created by Elaine Meng
It would be nice if we can search documentation that comes with …
4:41 PM Ticket #838 (Name selection command/GUI) closed by Conrad Huang
fixed: Completed.
4:40 PM Ticket #1067 (Automatically extend registration when using toolshed) closed by Conrad Huang
fixed: Completed. Currently, no statistics are being captured about …

Jun 1, 2018:

4:24 PM Ticket #1128 (Proxy server support) closed by pett
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 Conrad Huang
2:04 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:33 PM Ticket #1149 (bundles need test suites) created by Greg Couch
This ticket addresses pre-release testing, that is testing that is …
11:09 AM Ticket #1145 (Assign B-factors to added atoms) closed by Tom Goddard
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 Tom Goddard
fixed: Fixed.
7:00 AM Ticket #1148 (Repeat calls to 'cofr showpivot true' sheds pivot indicator colors) created by Tristan Croll
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 Tristan Croll
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 pett
fixed: I wouldn't normally bother with this kind of problem since …
3:54 PM Ticket #1146 (Bond rotation mouse mode broken) closed by pett
fixed
1:38 PM Ticket #783 (Integrate bundle help files with core help) closed by Greg Couch
fixed
11:05 AM Ticket #1146 (Bond rotation mouse mode broken) created by Tom Goddard
Using bond rotation mouse mode gives the following error in current …
6:18 AM Ticket #1145 (Assign B-factors to added atoms) created by Tristan Croll
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 Tristan Croll
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 Meghan.Driscoll@…
[…]
11:48 AM Ticket #1142 (after isolde install) created by kenneth.satyshur@…
[…]
11:48 AM Ticket #1141 (Unable to install clipper) created by kenneth.satyshur@…
[…]
10:45 AM Ticket #1133 (3D hardware stereo not working chimeraX in RHEL7) closed by Tom Goddard
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 Tom Goddard
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 Christian.Wetzel@…
[…]
7:07 AM Ticket #1139 (File drop: name 'p' is not defined) created by jcheng@…
[…]

May 23, 2018:

11:59 AM Ticket #1138 (Add NIfTI microscopy file format reader) created by Tom Goddard
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 Tom Goddard
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 Tom Goddard
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 Tom Goddard
Most light microscopy 3d images have z voxel size 5 times larger than …
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