![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
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 …
Jul 23, 2018:
- 9:36 PM Ticket #978 (Use mmCIF res->seq correspondence info) closed by
- fixed: Done.
- 6:50 PM ChangeLog edited by
- (diff)
- 6:36 PM Ticket #1205 (ChimeraX bug report submission) closed by
- not a bug: Testing crash reporter.
- 6:34 PM Ticket #1205 (ChimeraX bug report submission) created by
- […]
- 6:24 PM Ticket #1204 (ChimeraX bug report submission) closed by
- not a bug
- 6:23 PM Ticket #1204 (ChimeraX bug report submission) created by
- […]
- 5:10 PM Ticket #1203 (ChimeraX bug report submission) closed by
- not a bug
- 5:10 PM Ticket #1203 (ChimeraX bug report submission) created by
- […] setup.py
- 5:08 PM Ticket #1202 (ChimeraX bug report submission) closed by
- not a bug
- 5:04 PM Ticket #1202 (ChimeraX bug report submission) created by
- […]
Jul 20, 2018:
- 7:11 PM Ticket #1201 (Improve bug reporter tool) created by
- Port the Chimera bug reporting tool to ChimeraX.
- 7:05 PM Ticket #1200 (ChimeraX bug report submission) closed by
- not a bug
- 7:04 PM Ticket #1200 (ChimeraX bug report submission) created by
- […]
- 7:02 PM Ticket #1199 (ChimeraX bug report submission) closed by
- not a bug
- 6:57 PM Ticket #1199 (ChimeraX bug report submission) created by
- […]
- 3:21 PM Ticket #1182 (Error in addh at coordination sites) closed by
- fixed: I have committed a different fix for this. It works as far as I know, …
- 2:54 PM Ticket #1198 (ChimeraX bug report submission) closed by
- not a bug
- 2:54 PM Ticket #1198 (ChimeraX bug report submission) created by
- […]
- 2:17 PM Ticket #1197 (ChimeraX bug report submission) closed by
- not a bug
- 2:16 PM Ticket #1197 (ChimeraX bug report submission) created by
- […] bundle_info.xml
- 2:15 PM Ticket #1196 (ChimeraX bug report submission) closed by
- not a bug
- 2:15 PM Ticket #1196 (ChimeraX bug report submission) created by
- […]
- 2:05 PM Ticket #1195 (NMR ensemble connectivity terrible) created by
- Summary says it all. Example entries: 2hem, 1k5k PDB version looks fine.
- 1:11 PM Ticket #1194 (ChimeraX bug report submission) closed by
- not a bug
- 1:06 PM Ticket #1194 (ChimeraX bug report submission) created by
- […]
- 1:05 PM Ticket #1193 (ChimeraX bug report submission) closed by
- not a bug
- 12:57 PM Ticket #1193 (ChimeraX bug report submission) created by
- […]
- 12:56 PM Ticket #1192 (ChimeraX bug report submission) closed by
- not a bug
- 11:45 AM Ticket #1192 (ChimeraX bug report submission) created by
- […]
Jul 18, 2018:
- 6:04 PM Ticket #1169 ('new frame' trigger should still fire when no models open) closed by
- fixed: Fixed. "new frame" trigger now called as soon as ChimeraX starts even …
- 2:41 PM Ticket #1091 ("View all" doesn't play well with "cofr center showpivot true") closed by
- fixed: I made the view all and standard orientation toolbar buttons not …
- 2:19 PM Ticket #1191 (sym biomt: typos in import statement) closed by
- fixed: Hi David, I'm glad you're enjoying ChimeraX, mostly. :-) Yeah, 'sym …
- 2:03 PM 2018-06-28 edited by
- (diff)
- 2:03 PM 2018-06-28 edited by
- (diff)
- 10:41 AM Ticket #1108 (error on save image when object clipped near and far) closed by
- nonchimerax
- 10:09 AM Ticket #1003 (IHM "Invalid cross-device link") closed by
- fixed: Fixed. Made URL fetch put file directly in destination directory …
- 10:06 AM Ticket #1140 (problem with v0.6 and v0.7) closed by
- can't reproduce: No response from reporter.
- 10:04 AM Ticket #1143 (Toolbar clipped on high DPI display, Windows 10) closed by
- can't reproduce: We tested ChimeraX with a Windows 10 desktop machine connected to a 4K …
- 1:14 AM Ticket #1191 (sym biomt: typos in import statement) created by
- […]
Jul 17, 2018:
- 2:44 PM 2018-06-28 edited by
- (diff)
- 11:16 AM Ticket #1190 (Mac bundle builds fail when compiling C code) created by
- Clang complains and crashes if you ask it to compile a C file with …
Jul 16, 2018:
- 4:52 PM 2018-06-28 edited by
- (diff)
- 4:20 PM Ticket #1189 (Shader problem) closed by
- fixed: Fixed in tonight's build. Selection when ambient shadow lighting is …
- 3:37 PM Ticket #1189 (Shader problem) created by
- […]
- 1:35 PM Ticket #1176 (ChimeraX not opening) closed by
- fixed: Works for the user. Not sure what went wrong.
- 2:46 AM Ticket #1188 (ChimeraX should ask before registering itself as default application ...) created by
- It's something of an annoyance that ChimeraX automatically registers …
Jul 15, 2018:
- 4:26 PM Ticket #1186 (ChimeraX startup crash on Ubuntu 16.04) closed by
- nonchimerax: A similar fix should work for the Mac. Assuming the remote host is a …
Jul 13, 2018:
- 5:18 PM Ticket #1181 (ChimeraX on CentOS 7) closed by
- fixed: This bug has been fixed in the current daily build.
Jul 12, 2018:
- 5:20 PM Ticket #626 (If a volume is selected in the Models panel, Density Map Toolbar ...) closed by
- fixed: Okay, this is implemented (thanks for the code Tristan!), along with …
- 4:09 PM 2018-06-28 edited by
- (diff)
- 12:27 PM Ticket #1187 (AtomCenterOfRotationMode import error) closed by
- fixed: Fixed. Atomic module was moved and apparently those imports were not …
- 11:42 AM Ticket #1185 (ChimeraX startup crash on Ubuntu 16.04 (II)) closed by
- duplicate: follow up to #1186(!); added info to that ticket
- 4:31 AM Ticket #1187 (AtomCenterOfRotationMode import error) created by
-
Should be importing
cofrfromchimerax.std_commandsrather than … - 2:37 AM Ticket #1186 (ChimeraX startup crash on Ubuntu 16.04) created by
- […]
- 2:35 AM Ticket #1185 (ChimeraX startup crash on Ubuntu 16.04 (II)) created by
- […]
Jul 11, 2018:
- 5:47 PM Ticket #1183 (Swapaa adds deprotonated Cys) closed by
- fixed: Fixed. I've switched the swapaa mouse mode to use ideal coordinates …
- 1:49 PM Ticket #1184 (Implement "hbond true" flag for addh) created by
- As per Summary. PDBe interested in adding protons that maintain water …
Jul 10, 2018:
- 7:48 AM Ticket #1183 (Swapaa adds deprotonated Cys) created by
- At the moment the cysteine provided by swapaa lacks the HG atom. Valid …
- 6:10 AM Ticket #1182 (Error in addh at coordination sites) created by
- Traceback: […] Amending the offending lines (94-102) of …
Jul 9, 2018:
- 1:23 PM Ticket #1050 (Move core packages into bundles) closed by
- fixed: All modules moved.
- 1:12 PM Ticket #1178 (Handling of poor geometry in AddH) closed by
- fixed: Fixed. The atom-type-template dir wasn't getting installed.
- 11:04 AM Ticket #1181 (ChimeraX on CentOS 7) created by
- […]
- 10:35 AM Ticket #1180 (mmCIF reader forms no chains) created by
- At PDBe (EMBL-EBI) we are working on improving presentation of small …
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