Timeline



May 26, 2020:

8:40 PM Ticket #3325 (Crash when clicking on logged "silhouette false" command) created by kirk.n@…
[…]
6:28 PM Ticket #3324 (Wrong parent model assigned when shape command modelId given) created by goddard@…
[…]
6:20 PM Ticket #3323 (Side View should log a clipping command) created by Tom Goddard
Side View should log a clip command when the user moves a clip plane. …
6:17 PM Ticket #3292 (Circular dependency saving surface ("shape icosahedron"?)) closed by Tom Goddard
fixed: Fixed. Session save of surface geometry was incorrectly trying to …
6:14 PM Ticket #3200 (configfile/configparser not handling encoding) closed by Greg Couch
fixed: No response. Assume it's been fixed.
5:37 PM Ticket #3309 (some color commands should only target atomic models) closed by Tom Goddard
wontfix: MarkerSet is a Structure. There is another class called …
4:59 PM Ticket #3302 ("tool show" expanding to "toolshed show") closed by Greg Couch
fixed: Done. Also suppressed "tool" is a prefix of existing command …
4:25 PM Ticket #3296 (volume "subregion" keyword inconsistent with documentation) closed by Tom Goddard
wontfix: Named volume regions are a Chimera feature not currently supported in …
4:19 PM Ticket #3290 (selected_residues(session) very slow for large models) closed by Eric Pettersen
fixed: After looking at the code, I'm not looping in Python. The lesson is …
4:03 PM Ticket #3298 (Crash getting global interpreter lock) reopened by Tom Goddard
3:50 PM Ticket #3294 (Deleted color-blob check box still being used) closed by Tom Goddard
fixed: Fixed. Pick blobs mouse mode used after pick blobs gui panel was …
3:34 PM Ticket #3322 (Blast Protein has trouble with sequences that include UNK) created by Eric Pettersen
[…]
2:54 PM Ticket #3321 (remotecontrol subcommands on/off keywords inconsistent) created by Elaine Meng
Currently the REST subcommand takes start/stop and the XMLRPC one …
12:58 PM Ticket #3320 (No bug reported) created by chimerax-bug-report@…
[…]
11:34 AM Ticket #3319 (cartoon style modeHelix wrap: 'NoneType' object does not support item ...) created by Tristan Croll
[…]
11:12 AM Ticket #3318 (Shape command allows creating submodel without a parent model) created by goddard@…
[…]
11:06 AM Ticket #3317 (CCD fetch failures need to be cached) created by Tristan Croll
[…] big_membrane_lipids_only.cif​
11:04 AM Ticket #3314 (Non-functional selectors) closed by Eric Pettersen
not a bug: Hi Phil, The basic "name" command takes literally what you typed as …
10:29 AM Ticket #3310 (Session restore failure: ValueError: int is not allowed for map key) closed by Eric Pettersen
duplicate: Hi Doreen, This bug was fixed the day after the version you are …
10:23 AM Ticket #3316 (Test if bug report log contains all commands) closed by Tom Goddard
not a bug: All commands in this test seemed to make it into the bug report log.
10:18 AM Ticket #3308 (User-supplied template does not match the residue) closed by Eric Pettersen
duplicate
10:17 AM Ticket #3316 (Test if bug report log contains all commands) created by goddard@…
[…]
10:13 AM Ticket #3307 (Model panel, list index out of range, restoring session) closed by Eric Pettersen
duplicate: Similar to #3279 -- same user, related session.
10:10 AM Ticket #3305 (Save dialog failure) closed by Eric Pettersen
duplicate: Hi Raoul, This problem was fixed in the build immediately after the …
9:54 AM Ticket #3304 (safeguard chain IDs) closed by Eric Pettersen
wontfix: Hi Tristan, I do not envision "setattr" as being the command for …
9:40 AM Ticket #3315 (Lighting dark in stereo mode) created by kenneth.satyshur@…
Begin forwarded message: From: Kenneth Satyshur Subject: …
9:39 AM Ticket #3280 (Error saving session in Clipper symmetry, CORE_STATE_VERSION gone) closed by Tristan Croll
fixed: All sorted. Saving and restoring happily again.
9:06 AM Ticket #3311 (Installing ISOLDE in old ChimeraX version) closed by Tristan Croll
fixed
6:36 AM Ticket #3314 (Non-functional selectors) created by phil.cruz@…
[…] InducedFit_model1_rec.mae​
6:09 AM Ticket #3313 ("Vestigial" ViewDockX can interfere with session restore) created by phil.cruz@…
[…] ViewDocX_bug.cxs​
5:35 AM Ticket #3312 (Help Viewer crash) created by lmukhame@…
[…]
3:08 AM Ticket #3311 (Installing ISOLDE in old ChimeraX version) created by nicolas.floquet@…
[…]
2:38 AM Ticket #3310 (Session restore failure: ValueError: int is not allowed for map key) created by doreen.henkel92@…
[…] chimera bug opening csx file.PNG​
2:06 AM Ticket #3309 (some color commands should only target atomic models) created by Tristan Croll
[…]

May 25, 2020:

6:13 PM Ticket #3308 (User-supplied template does not match the residue) created by chimerax-bug-report@…
[…]
5:51 PM Ticket #3307 (Model panel, list index out of range, restoring session) created by chimerax-bug-report@…
[…]
5:30 PM Ticket #3306 (ChimeraX startup: unsupported locale setting) created by tony.schaefer@…
[…]
4:28 PM Ticket #3305 (Save dialog failure) created by raoulmartin@…
[…]
3:55 PM Ticket #3284 (Unknown command: linux xdg-install system true) closed by Greg Couch
fixed: Sorry about that. The fixed will be in the next release candidate, …
2:49 PM Ticket #3304 (safeguard chain IDs) created by Tristan Croll
[…]
12:49 PM Ticket #3303 (Weird copy/paste behavior) created by Elaine Meng
[…]
12:46 PM Ticket #3302 ("tool show" expanding to "toolshed show") created by Elaine Meng
[…]
9:43 AM Ticket #3299 (unexpected unindent running Volume Viewer) closed by Tom Goddard
duplicate: Was fixed a week ago. Get current ChimeraX.
9:43 AM Ticket #3293 (unexpected unindent running Volume Viewer) closed by Tom Goddard
duplicate: Was fixed a week ago. Get current ChimeraX build.
9:38 AM Ticket #3301 (Model panel, list index out of range, restoring session) closed by Eric Pettersen
duplicate: Similar to #3279 -- same user, related session. Would be nice if …
9:30 AM Ticket #3298 (Crash getting global interpreter lock) closed by Eric Pettersen
can't reproduce
9:12 AM Ticket #3286 (ISOLDE: KeyError in find_glycan_template_name_and_link) closed by Tristan Croll
fixed: Arg! Didn't notice that this was an anonymous report. Sigh. Closing as …
9:06 AM Ticket #3291 (Model panel, list index out of range, restoring session) closed by Eric Pettersen
duplicate: Exact duplicate of #3279 (same user/session)
9:02 AM Ticket #3289 (Model panel, list index out of range, restoring session) closed by Eric Pettersen
duplicate: Exact duplicate of #3279 (same user/session)
9:00 AM Ticket #3288 (Model panel, list index out of range, restoring session) closed by Eric Pettersen
duplicate: Exact duplicate of #3279 (same user/session)
8:59 AM Ticket #3287 (Model panel, list index out of range, restoring session) closed by Eric Pettersen
duplicate: Exact duplicate of #3279 (same user/session)
8:57 AM Ticket #3300 (ISOLDE and reporting error) closed by Tristan Croll
fixed: The new ISOLDE builds (once released) will give more helpful error …
8:41 AM Ticket #3301 (Model panel, list index out of range, restoring session) created by chimerax-bug-report@…
[…]
4:47 AM Ticket #3300 (ISOLDE and reporting error) created by DLMLEN001@…
[…]
2:04 AM Ticket #3299 (unexpected unindent running Volume Viewer) created by wpp15@…
[…] emd_9333_msk_1.map​

May 24, 2020:

7:21 PM Ticket #3298 (Crash getting global interpreter lock) created by chimerax-bug-report@…
[…]
4:35 PM Ticket #3297 (Error opening grayscale + alpha 2D image) created by goddard@…
[…] gray_alpha.tif​
1:37 AM Ticket #3296 (volume "subregion" keyword inconsistent with documentation) created by Tristan Croll
[…]
1:27 AM Ticket #3295 (Help Viewer back-button bug) created by Tristan Croll
[…]
12:51 AM Ticket #3294 (Deleted color-blob check box still being used) created by chimerax-bug-report@…
[…]

May 23, 2020:

11:46 AM Ticket #3293 (unexpected unindent running Volume Viewer) created by borukhse@…
[…]
9:38 AM Ticket #3292 (Circular dependency saving surface ("shape icosahedron"?)) created by chimerax-bug-report@…
[…]
5:52 AM Ticket #3291 (Model panel, list index out of range, restoring session) created by chimerax-bug-report@…
[…]
4:14 AM Ticket #3290 (selected_residues(session) very slow for large models) created by Tristan Croll
From #3285. For 3j3y, with all atoms selected: […] The actual …

May 22, 2020:

8:48 PM Ticket #3289 (Model panel, list index out of range, restoring session) created by chimerax-bug-report@…
[…]
6:25 PM Ticket #3288 (Model panel, list index out of range, restoring session) created by chimerax-bug-report@…
[…]
6:16 PM Ticket #3275 (Registration server unavailable) closed by Conrad Huang
fixed: The registration script should be able to handle UTF-8 characters now. …
6:12 PM Ticket #3287 (Model panel, list index out of range, restoring session) created by chimerax-bug-report@…
[…]
5:00 PM Ticket #1885 (error using BLOSUM100 in blast) closed by Conrad Huang
fixed: Fixed in 7510c8922. The list of supported similarity …
3:01 PM Ticket #3286 (ISOLDE: KeyError in find_glycan_template_name_and_link) created by chimerax-bug-report@…
[…]
2:59 PM Ticket #3285 (Slow graphics updates) created by Tristan Croll
[…]
2:21 PM Ticket #3234 (ISOLDE Tool Shed install button not appearing) closed by Greg Couch
fixed: Heard from Tristan that this was fixed. If not, please let us know.
1:57 PM Ticket #3232 (Tool Shed download problem) closed by Greg Couch
fixed: The production toolshed has been updated with the new code.
1:47 PM Ticket #3281 (Garbled PostiveIntArg error message) closed by Greg Couch
fixed: Fixed the error message.
11:59 AM Ticket #3284 (Unknown command: linux xdg-install system true) created by huatiger3@…
[…] 20200522_Chimerax_ubuntu_20_04_install_fail_log​
11:23 AM Ticket #3283 (Truncated fetched file produces error when fetched again) created by goddard@…
[…]
11:18 AM Ticket #1311 (Windows 10 display scaling gives wrong GUI text sizes) closed by Tom Goddard
fixed: Font sizes currently look reasonable at 100%, 125% and 175% scaling on …
11:13 AM Ticket #1134 (VR gui panel does not work hidden on desktop) closed by Tom Goddard
fixed: VR now shows each ChimeraX tool and a separate pane and those panels …
10:55 AM Ticket #3251 (Another clEnqueueReadBuffer problem) closed by Tristan Croll
fixed: Great! I'll go ahead and close this then.
10:30 AM Ticket #151 (Rendering ribbon with stick is slow) closed by Tom Goddard
can't reproduce: Retried this test on a newer Mac laptop with larger system 4v88, …
10:24 AM Ticket #61 (Rendering takes minutes, Mac Nvidia Geforce GT 330M graphics) closed by Tom Goddard
nonchimerax: The computers that have these extremely limited graphics seem rare …
10:20 AM Ticket #947 (Image save only includes lower left quadrant, Mac retina display) closed by Tom Goddard
can't reproduce: This was a macOS graphics driver issue. I have not seen it reported …
10:18 AM Ticket #1041 (Surprising slowdown when drawing multiple drawings) closed by Tom Goddard
fixed: Seems performance was made adequate with some bounding box optimization.
10:12 AM Ticket #2408 (Cannot use Lenobo explorer for VR) closed by Tom Goddard
can't reproduce: No response from user debugging VR setup.
10:09 AM Ticket #2536 (Tug mouse mode bad allocation error) closed by Tom Goddard
fixed: ChimeraX now uses the updated OpenMM 7.4.1
10:08 AM Ticket #2566 (Can't start ChimeraX) closed by Tom Goddard
can't reproduce: Some kind of OpenGL / graphics driver problem on reporter's computer. …
10:06 AM Ticket #2565 (Problems using previously fetched files) closed by Tom Goddard
can't reproduce: Haven't seen this reported again. So I suspect improvements to macOS …
9:52 AM Ticket #2961 (Tips for remote use) closed by Tom Goddard
wontfix: In general my recommendation for running ChimeraX remotely is "Don't …
9:43 AM Ticket #3037 (Selection problems) closed by Tom Goddard
can't reproduce: Could be that the default framebuffer depth was not 24 as assumed by …
9:39 AM Ticket #3222 (During ChimeraX quit: Could not make graphics context current) closed by Tom Goddard
can't reproduce: I added code so that if an OpenGL error occurs when deleting a Drawing …
9:36 AM Ticket #3239 (Graphics window banks to gray) closed by Tom Goddard
can't reproduce
9:21 AM Ticket #3282 (Add mcopy command) created by olibclarke@…
The mcopy command is useful for replacing a model in a figure and …
7:38 AM Ticket #3281 (Garbled PostiveIntArg error message) created by Tristan Croll
[…]
6:21 AM Ticket #3280 (Error saving session in Clipper symmetry, CORE_STATE_VERSION gone) created by Tristan Croll
[…]

May 21, 2020:

7:00 PM Ticket #3278 (Bogus capitalization of SimpleXMLRPCServer.__Init__) closed by Tom Goddard
fixed: Fixed. Jeez, I guess I managed to upcase the word with an errant key …
6:49 PM Ticket #3279 (Prevent bad model hierarchies from being formed) created by chimerax-bug-report@…
[…]
5:52 PM Ticket #2080 (Awkward text copy from Help Viewer (HTML widgets?)) closed by Eric Pettersen
fixed: Was able to move the log window's workaround into the base class, but …
5:39 PM Ticket #3278 (Bogus capitalization of SimpleXMLRPCServer.__Init__) created by Elaine Meng
[…]
4:03 PM Ticket #3277 (Import error running Linux installer) closed by Eric Pettersen
fixed: Hi John, Thanks for reporting this problem. It is fixed now and the …
3:52 PM Ticket #3274 (Re: [chimerax-users] Recreating views) closed by Eric Pettersen
invalid: intended for chimerax-users
3:36 PM Ticket #3277 (Import error running Linux installer) created by huatiger3@…
[…] 20200521_Chimerax_ubuntu_20_04_install_log​
2:46 PM Ticket #3270 (Bfactor sharpening on resampled map) closed by Tom Goddard
not a bug: This is not a bug. I attached an image showing that the resampling …
2:21 PM Ticket #3257 (unable to reopen data from file history) closed by Eric Pettersen
fixed: I wound up change FileHistory as per Tom's suggestion to map the old …
12:50 PM Ticket #3276 (nucleotide sugar-tubes disconnected from ribbon in restored session) created by Elaine Meng
open 2bna save nuctest.cxs close open nuctext.cxs .... now …
12:28 PM Ticket #3275 (Registration server unavailable) created by eugenio.vazquez@…
[…]
11:24 AM Ticket #3272 (MAV: region name is None) closed by Eric Pettersen
fixed: If the setting for showing the selection region was off, then fetching …
10:35 AM Ticket #2712 (A lot of array size mismatches after deletions) closed by Tom Goddard
can't reproduce: This does not look like a ribbon error. It was caused by deleting …
10:26 AM Ticket #3213 (REST: broken pipe) closed by Conrad Huang
fixed: The fix worked!
10:05 AM Ticket #3273 (Missed a "toolshed show" conversion) closed by Greg Couch
fixed: That was fixed shortly after you downloaded the candidate release. …
9:47 AM Ticket #3274 (Re: [chimerax-users] Recreating views) created by Tristan Croll
[…]
2:30 AM Ticket #3273 (Missed a "toolshed show" conversion) created by bssfh@…
[…]

May 20, 2020:

9:38 PM Ticket #3272 (MAV: region name is None) created by chimerax-bug-report@…
[…]
6:27 PM Ticket #3271 (Line-ending issues for resaved PDB files) created by jonathan@…
[…] pdb-export-eol-test-case.zip​
6:00 PM Ticket #3270 (Bfactor sharpening on resampled map) created by olibclarke@…
[…] Screenshot 2020-05-20 20.56.53.png​
5:04 PM Ticket #3064 (Adding images and descriptions to RBVI bundles) closed by Conrad Huang
fixed: "maestro" is already on the toolshed. "speech" should not see the …
4:59 PM Ticket #2917 (BlaST web service: No alias or index file found for protein database) closed by Conrad Huang
fixed: Fixed in b62257089. Instead of catching one specific …
4:52 PM Ticket #3014 (Blast Protein tool: threading) reopened by Elaine Meng
This is an RFE not a bug report. Request is to allow entering …
4:43 PM Ticket #3014 (Blast Protein tool: threading) closed by Conrad Huang
not a bug: Currently, the Blast Protein tool can only use the sequence from a …
4:32 PM Ticket #2373 (Registration failure) closed by Conrad Huang
can't reproduce: Not sure where a self-signed cert would be used when connecting to …
4:30 PM Ticket #2993 (KeyError picking ribbon) closed by Conrad Huang
wontfix: Ribbon code has been completely revamped.
4:21 PM Ticket #3079 (Registration failure (while plato was down)) closed by Conrad Huang
fixed: Fixed in d60748b6c. Looks like a "Connection refused" …
4:03 PM Ticket #3256 (ViewDockX save broken) closed by Conrad Huang
fixed: Fixed in 1baab4c05. Some code got indented too far and …
3:29 PM Ticket #3267 (REST https responses garbled) closed by Conrad Huang
not a bug: The server got gobbledygook on input and logged it as such. Not sure …
3:25 PM Ticket #3268 (ssl.SSLError starting REST server with 'ssl true') closed by Conrad Huang
fixed: Fixed in 82e20c048. The code works, but uses a …
2:54 PM Ticket #2818 (Improve sample bundle code) closed by Eric Pettersen
fixed: Hi Tristan, Thanks for this -- it's really excellent and it must have …
12:57 PM Ticket #3191 (remove dead I/O code) closed by Eric Pettersen
fixed
9:50 AM Ticket #3269 (Custom multitouch trackpad bindings) created by Tristan Croll
This has been on the to-do list for a while, and I was recently …
9:36 AM Ticket #3268 (ssl.SSLError starting REST server with 'ssl true') created by goddard@…
[…]
9:27 AM Ticket #3267 (REST https responses garbled) created by goddard@…
[…]
8:38 AM Ticket #3262 (Problems both saving and restoring nucleotides) closed by Greg Couch
duplicate: duplicate of #3263
8:03 AM Ticket #3266 (RFE: have matchmaker maintain original SS assignments) created by Tristan Croll
[…]
7:55 AM Ticket #3264 (glTF save error) closed by Eric Pettersen
fixed: Hi Jonathan Thanks for reporting this problem. I have just fixed it …
7:53 AM Ticket #3265 (glTF save error) closed by Eric Pettersen
fixed: Hi Thibault, Thanks for reporting this problem. I have just fixed it …
1:05 AM Ticket #3265 (glTF save error) created by thibault.tubiana@…
[…] error_chimeraX.txt​
12:44 AM Ticket #3264 (glTF save error) created by jonathan@…
[…] adenine.mol​

May 19, 2020:

7:09 PM Ticket #3252 (DCD "append" not working) closed by Tom Goddard
fixed: Fixed. Reading DCD coordinates with replace false was ignoring the …
6:53 PM Ticket #3263 (problems both saving and restoring nucleotides) created by Fengwei.Zheng@…
[…]
6:53 PM Ticket #3262 (Problems both saving and restoring nucleotides) created by chimerax-bug-report@…
[…]
6:46 PM Ticket #3261 (Make model-panel coloring issue command) created by olibclarke@…
[…]
6:19 PM Ticket #3255 (labels for hidden objects not auto-hiding) closed by Tom Goddard
fixed: Fixed. Changed tracking of atom display changed 7 weeks ago (#3000) …
6:14 PM Ticket #3253 (3 wishes) closed by Eric Pettersen
duplicate: I divided these into separate tickets so that they could be assigned …
6:11 PM Ticket #3260 ('clipping' mouse mode should section) created by olibclarke@…
The right mouse mode "clipping", when set to "clip screen planes" in …
6:10 PM Ticket #3259 (Saved tool positions not preserving tabbing) created by olibclarke@…