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Timeline
Aug 23, 2018:
- 2:50 PM 2018-08-23 created by
- 2:08 PM DeveloperMeetings edited by
- (diff)
- 1:16 PM Ticket #1266 (crosslinks and sequence viewer problems) closed by
- fixed: Hi Pascal, Thanks for reporting the problem. The issue was that some …
- 12:31 PM Ticket #1265 (Color command: min() arg is an empty sequence) closed by
- fixed: Fixed. Color by bfactor command with no atoms raised this error.
- 4:12 AM Ticket #1266 (crosslinks and sequence viewer problems) created by
- […]
- 3:39 AM Ticket #1265 (Color command: min() arg is an empty sequence) created by
- […]
Aug 22, 2018:
- 3:48 PM Ticket #1264 (Drawing.selected inaccurate) created by
- If I open any model (e.g. 1a0m) and 'sel #1', the model instance's …
- 2:37 PM Ticket #1263 (Setting view background color changes clipping) closed by
- not a bug: You set the background color RGBA to (255,255,255,1). This is almost …
- 2:28 PM Ticket #1261 (OpenGL error: invalid value) closed by
- fixed: I don't know why you are pasting a sequence into the ChimeraX …
- 2:21 PM Ticket #1262 (Associating structures with sequence: local variable 'best_match_map' ...) closed by
- fixed: Fixed; one of the changes necessitated when translating the …
- 12:10 PM ChangeLog edited by
- (diff)
- 11:29 AM Ticket #1263 (Setting view background color changes clipping) created by
- […] Screen Shot 2018-08-22 at 2.28.01 PM.png
- 10:26 AM Ticket #1262 (Associating structures with sequence: local variable 'best_match_map' ...) created by
- […]
- 1:48 AM Ticket #1261 (OpenGL error: invalid value) created by
- […] åºå åæåå ä¿®æ¹ åçé.doc
Aug 21, 2018:
- 2:13 PM Ticket #1260 (Clipping after changing lighting option) closed by
- can't reproduce: I change the lighting all the time and have never seen this clipping …
- 2:03 PM Ticket #1260 (Clipping after changing lighting option) created by
- […] [[Image(...)]] [[Image(...)]]
Aug 20, 2018:
Aug 16, 2018:
- 10:39 AM Ticket #1258 (Partial protein residues not classified as protein) created by
- In ChimeraX , 6c2f GLY 147 and PRO 215 are not classified as …
- 10:28 AM Ticket #1257 (Module can't find shared lib) closed by
- duplicate: duplicate of #1256; adding reporter to recipient list for that ticket
- 10:26 AM Ticket #1255 (OS X 10.10 symbol (_clock_gettime) problem) closed by
- wontfix: We don't support OS X 10.10
- 6:46 AM Ticket #1257 (Module can't find shared lib) created by
- […]
Aug 15, 2018:
- 4:10 PM Ticket #1256 (Module can't find shared lib) created by
- […]
- 1:56 PM Ticket #1255 (OS X 10.10 symbol (_clock_gettime) problem) created by
- […]
- 10:22 AM Ticket #1253 (Remove CPK colours from list of possible chain colours) closed by
- fixed: Fixed. I replace 5 default chain colors (chains I,O,N,2,3) that were …
Aug 14, 2018:
- 5:08 PM Ticket #1254 (Too many bundle cache startup messages) created by
- […]
- 1:08 PM Ticket #1252 (Depth cueing fades to black, not background colour) closed by
- fixed: Fixed. Was broken when lighting opengl code was changed to use …
- 12:44 PM Ticket #1253 (Remove CPK colours from list of possible chain colours) created by
- When loading a large model with lots of chains, some chains will end …
- 11:38 AM Ticket #1223 (Cannot instantiate Python class corresponding to C++ ...) closed by
- can't reproduce: Haven't been seeing this crash recently. Need some kind of vaguely …
- 8:30 AM Ticket #1252 (Depth cueing fades to black, not background colour) created by
- Not sure when this started happening again, but it's happening in the …
Aug 13, 2018:
- 3:30 PM Ticket #1248 (atom spec balloon: index is out of bounds) closed by
- can't reproduce: Mouse hover over an atom is producing an out of range atom index 776 …
- 10:29 AM Ticket #1251 (Crash in chem_group::find_5ring_OR2) closed by
- can't reproduce: There is no direct call to free() in that routine, so need more info.
- 10:19 AM Ticket #1249 (atom spec balloon: index is out of bounds) closed by
- duplicate
- 5:29 AM Ticket #1251 (Crash in chem_group::find_5ring_OR2) created by
- […]
Aug 10, 2018:
- 3:03 PM Ticket #1118 (deleting residues from a chain leads to erroneous PDB) closed by
- fixed: mid-chain deletions now form a missing-structure pseudobond as appropriate
- 10:57 AM Ticket #1249 (atom spec balloon: index is out of bounds) created by
- […]
- 10:57 AM Ticket #1248 (atom spec balloon: index is out of bounds) created by
- […]
Aug 9, 2018:
- 3:17 PM Ticket #1247 (ERROR: Tool "Command Line Interface" failed to start) closed by
- fixed: Catch the JSON decode error (due to the corrupted file) and treat the …
- 1:53 PM Ticket #1246 ('Update your driver' should be modal) closed by
- fixed: Fixed. If opengl context has inadequate version the error is shown at …
- 11:16 AM Ticket #1247 (ERROR: Tool "Command Line Interface" failed to start) created by
- […]
- 10:53 AM Ticket #1240 ('NoneType' object has no attribute 'apply_without_translation') closed by
- fixed: This was fixed several days ago.
Aug 8, 2018:
- 5:45 PM Ticket #1246 ('Update your driver' should be modal) created by
- […]
- 3:37 PM Ticket #1245 (Fragment-based model building in density) created by
- Would like to be able to find short peptide fragments from all …
- 3:34 PM Ticket #1244 (Local interactive b-factor sharpening for density maps) created by
- Would like to be able to interactive adjust amount of b-factor …
- 3:32 PM Ticket #1243 (Allow ambient shadowing on transparent surfaces) created by
- Would like ambient shadowing on transparent surfaces. Currently …
- 3:28 PM Ticket #1242 (Straight helix tubes) created by
- Want to show straight helix tubes in cartoon display style.
- 3:25 PM Ticket #1241 (Supersample density maps) created by
- To show x-ray and cryoEM meshes that appear smoother it is nice to use …
- 2:20 PM Ticket #1240 ('NoneType' object has no attribute 'apply_without_translation') created by
- […]
- 11:26 AM Ticket #1227 (atom spec syntax for model but not submodels) closed by
- fixed: Implemented.
- 10:53 AM ChangeLog edited by
- (diff)
- 10:52 AM ChangeLog edited by
- (diff)
Aug 7, 2018:
- 3:05 PM Milestone 0.7 completed
- == Chimera Features == Innovation * Virtual reality parallel graphics …
- 12:52 PM Ticket #1115 (H-bonds found between metal-ligating heteroatoms) closed by
- fixed: Now screens out h-bonds where the lone pair is already committed to …
- 11:30 AM Ticket #904 (stitch chain fragments together) closed by
- fixed: Upon further review of the attached file, don't want to put …
Aug 6, 2018:
- 7:28 PM Ticket #1235 ('camera_position' is None) closed by
- fixed: Fixed. Mouse rotation was throwing errors in VR due to recent change …
- 1:57 PM Ticket #1180 (mmCIF reader forms no chains) closed by
- fixed: mmCIF chain id is now preserved if possible in mmCIF output.
- 1:37 PM Ticket #1239 ("command line" string not suitable for command line) closed by
- fixed
- 11:52 AM Ticket #1239 ("command line" string not suitable for command line) created by
- […]
- 11:37 AM Ticket #1238 ('camera_position' is None) closed by
- duplicate: dup of #1235
- 11:36 AM Ticket #1237 ('camera_position' is None) closed by
- duplicate: dup of #1235
- 11:35 AM Ticket #1236 ('camera_position' is None) closed by
- duplicate: dup of #1235
Aug 3, 2018:
- 3:00 PM Ticket #1238 ('camera_position' is None) created by
- […]
- 3:00 PM Ticket #1237 ('camera_position' is None) created by
- […]
- 2:54 PM Ticket #1236 ('camera_position' is None) created by
- […]
- 2:31 PM Ticket #1235 ('camera_position' is None) created by
- […]
- 12:55 PM Ticket #1231 (Slow rotation after presets used) closed by
- fixed
- 12:55 PM Ticket #1179 (Nucleotides slows other rendering) closed by
- fixed: Fixed. Duplicate of #1231.
- 10:07 AM Ticket #1234 (Showing volume bounding box causes traceback) closed by
- fixed: Fixed. A week or two ago I made Drawings require a name, the name can …
- 9:57 AM Ticket #1233 (Grid_Data applies rotation and skew in wrong order?) closed by
- not a bug: The rotation in Grid_Data is not for permuting axes, it is for …
- 6:09 AM Ticket #1234 (Showing volume bounding box causes traceback) created by
- - Load a volume - click the "Show outline box" button Traceback: […]
- 5:56 AM Ticket #1233 (Grid_Data applies rotation and skew in wrong order?) created by
- Unless I'm missing something obvious... The background is that while …
Aug 2, 2018:
- 5:46 PM Ticket #1232 (Script that loads many files replaces all of file history) created by
- Running a script that loads many PDB files fills up file history. …
- 5:41 PM Ticket #1231 (Slow rotation after presets used) created by
- […]
- 4:52 PM Ticket #1224 (Unable to save "NucleotideState") closed by
- fixed: Remove nucleotides state manager when there are no more structures …
- 3:56 PM Ticket #1230 (Better bundle_builder support for Cython) created by
- Need some way to inform Cython compile about headers and libs in other …
- 3:51 PM Ticket #1229 (Eliminate is_het res attribute) created by
- is_het is format specific and should be handled by the appropriate …
- 3:47 PM Ticket #1228 (Run Modeller) created by
- Model single or multiple chains from one or more alignments.
- 3:06 PM Ticket #1227 (atom spec syntax for model but not submodels) created by
- The syntax #!model-num was grudgingly agreed upon.
- 3:03 PM Ticket #904 (stitch chain fragments together) reopened by
- 3:02 PM Ticket #904 (stitch chain fragments together) closed by
- fixed
- 2:52 PM 2018-08-02 created by
- 2:16 PM Ticket #1226 (RFE: some way to get back initial default cartoon style) created by
- I'd thought that if we had cartoon-style presets (#297) that one of …
- 2:15 PM DeveloperMeetings edited by
- (diff)
- 1:40 PM 2018-06-28 edited by
- (diff)
- 1:35 PM Ticket #1225 (RFE: synonyms "round" "square" for cartoon style xsection) created by
- I'd documented in "cartoon style" that xsection "round" was a synonym …
- 1:31 PM Ticket #1224 (Unable to save "NucleotideState") created by
- […] bug2.cxs
- 12:13 PM Ticket #1222 (making window small after show/hide Side View makes molecule black) closed by
- fixed: Fixed. I changed the opengl lighting implementation about 4 weeks ago …
- 12:11 PM Ticket #1223 (Cannot instantiate Python class corresponding to C++ ...) created by
- […] carstyles.cxs
- 11:37 AM Ticket #1222 (making window small after show/hide Side View makes molecule black) created by
- This is bizarre.... apparently it is necessary to show and then close …
Aug 1, 2018:
- 5:02 PM ChangeLog edited by
- (diff)
- 4:59 PM Ticket #1184 (Implement "hbond true" flag for addh) closed by
- fixed: 'hbond true' (i.e. the default) flag implemented. Available in next …
- 4:00 PM Ticket #1221 (devel commands needs to use docker/singularity for Linux builds) created by
- To ensure that binary Linux bundles work on other systems, they all …
- 3:52 PM ChangeLog edited by
- (diff)
- 11:55 AM Ticket #1219 (UnicodeEncodeError writing WaveFront OBJ) closed by
- fixed: Fixed. The atom distance labels caused the error saving OBJ format …
- 10:45 AM Ticket #1220 (Bad atomic import) closed by
- fixed: This problem was fixed yesterday and does not occur in the current …
- 10:43 AM Ticket #1220 (Bad atomic import) created by
- […]
- 10:36 AM Ticket #1218 (can't report a bug) closed by
- fixed: Fixed. Don't raise error in bug reporter when getting opengl version …
- 10:22 AM Ticket #1217 (ChimeraX bug report submission) closed by
- can't reproduce
Jul 31, 2018:
- 11:51 PM Ticket #1119 (Misleading pseudobond at RNA chain break in mmCIF 5an9) closed by
- fixed: Fixed. For residues with templates and known linking atoms, if the …
- 8:00 PM Ticket #1219 (UnicodeEncodeError writing WaveFront OBJ) created by
- […]
- 4:59 PM Ticket #1218 (can't report a bug) created by
- And in this case, reporting a bug should not be an option. When …
- 2:49 PM Ticket #1217 (ChimeraX bug report submission) created by
- […]
- 1:11 PM Ticket #1215 (Make install in atomic module does not detect changes) closed by
- can't reproduce: Tried to reproduce this with T.G.'s help and couldn't. If some …
- 11:14 AM Ticket #1216 (Old atomic import) closed by
- fixed: The Cython code had some 'core.atomic' imports lurking in it, now removed.
- 10:09 AM Ticket #1216 (Old atomic import) created by
- […]
- 10:03 AM Ticket #1215 (Make install in atomic module does not detect changes) created by
- A "make install" in the atomic module sometimes does not detect …
- 9:54 AM Ticket #1214 (ChimeraX bug report submission) closed by
- not a bug
- 9:40 AM Ticket #1214 (ChimeraX bug report submission) created by
- […]
Jul 30, 2018:
- 11:12 AM Ticket #1213 (AddH: unexpected None residue in sequence) closed by
- fixed: Thanks for reporting this. The new set_input_seq_info() API wasn't …
- 5:41 AM Ticket #1213 (AddH: unexpected None residue in sequence) created by
- […]
Jul 27, 2018:
- 9:25 AM Ticket #1207 (CentOS/RedHat 7 specific distribution) closed by
- duplicate: Will keep track of progress in #473.
- 9:23 AM Ticket #1174 (Bogus missing-structure pseudobonds in 2duf) closed by
- fixed: The code was figured out the connecting atoms, but a …
- 12:06 AM Ticket #1212 (opening 4b3o can produce KeyError generating chain descriptions) created by
- […]
Jul 26, 2018:
- 7:30 PM Ticket #1210 (ChimeraX bug report submission) closed by
- fixed: Changed logic for detecting missing entity_poly_seq table. Structure …
- 4:02 PM Ticket #1211 (show nucleotide representations for modified nucleic acids) created by
- Doesn’t the mmCIF file or some lookup table available from wwPDB say …
- 2:10 PM Ticket #1210 (ChimeraX bug report submission) created by
- […]
- 1:03 PM Ticket #1209 (cartoon preset undisplays too much) created by
- For 2adw, selecting the cartoon preset appears to hide NCY and N2C …
- 10:35 AM Ticket #1208 (Error closing Active Tools tool) created by
- […]
- 2:51 AM Ticket #1207 (CentOS/RedHat 7 specific distribution) created by
- Would it be possible to provide a CentOS-friendly tarball on the …
Jul 24, 2018:
- 12:20 PM Ticket #1206 (error trying to show Side View) closed by
- fixed: Fixed.
- 10:35 AM Ticket #1206 (error trying to show Side View) created by
- UCSF ChimeraX version: 0.7 (2018-07-23) OpenGL version: 4.1 …
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