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Timeline
Jun 1, 2017:
- 11:44 PM BundleReformatting edited by
- (diff)
- 3:08 PM 2017-06-01 edited by
- (diff)
- 2:00 PM 2017-06-01 created by
- 1:57 PM DeveloperMeetings edited by
- (diff)
- 12:04 PM Ticket #701 (Add buttons to toggle map or atomic structure display) created by
- Begin forwarded message: From: Oliver Clarke Subject: …
- 6:33 AM Ticket #700 (Toolshed dependency issue) created by
- My ISOLDE plugin is dependent upon my Clipper plugin. In the ISOLDE …
- 12:54 AM Ticket #699 (core.commands.rename issues) created by
- If I create an empty model first: […] ... then load a structure …
May 31, 2017:
- 11:49 PM Ticket #697 (cif file saved from model with children causes segmentation fault on load) closed by
- fixed: There was a bug in the code that faked the missing entity_poly_seq …
- 9:08 PM BundleReformatting edited by
- (diff)
- 9:05 PM BundleReformatting edited by
- (diff)
- 2:57 PM BundleReformatting edited by
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- 2:39 PM Ticket #274 (Select through transparent surface or mesh) closed by
- fixed: Fixed. The default behavior is now to select through transparent …
- 2:33 PM Ticket #569 (Show selected atoms under transparent surface) closed by
- fixed: Fixed. The selection outlines for objects behind transparent surfaces …
- 2:01 PM BundleReformatting edited by
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- 2:00 PM BundleReformatting edited by
- (diff)
- 1:58 PM BundleReformatting edited by
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- 12:10 PM Ticket #698 (Make slider record button bring up movie option panel) created by
- The coordinate set slider, map series slider, model series slider, and …
- 10:02 AM Ticket #697 (cif file saved from model with children causes segmentation fault on load) created by
- Two-parter here: 1. If I have an AtomicStructure with child models …
- 9:54 AM Ticket #696 (File/save causing segmentation fault in Linux) created by
- Doesn't appear related to anything I've done (crashes even in a …
- 3:23 AM Ticket #695 (Ribbon should not affect Atom.hide for structures with no ribbons) created by
- I have a class (subclassed from Structure) used to draw position …
May 30, 2017:
- 2:09 PM Ticket #694 (Add C-alpha trace depictions) created by
- Begin forwarded message: From: Oliver Clarke Subject: …
- 12:56 PM Ticket #693 (Add next / previous map buttons) created by
- Begin forwarded message: From: Oliver Clarke <> Subject: …
- 12:54 PM Ticket #692 (Add a scale bar tool) created by
- Begin forwarded message: From: Oliver Clarke Subject: …
- 10:53 AM Ticket #691 ("atomic" keyword to "open" for structures) created by
- Controls whether the result is a Structure or an AtomicStructure
May 29, 2017:
- 8:39 AM Ticket #690 (Custom atom/residue properties?) created by
- There are various situations where one might want to associate custom …
May 26, 2017:
- 9:52 AM Ticket #683 (atomspec_has_atoms() is inconsistently applied.) closed by
- fixed: Using atom.hide = True did the trick.
May 25, 2017:
- 5:45 PM Ticket #688 (Toolshed 'author' link: TemplateSyntaxError) closed by
- fixed
- 4:40 PM Ticket #689 (Non-canonical H-bonds) created by
- Extend the H-bond detection functionality to include non-canonical …
- 4:24 PM BundleReformatting created by
- 4:05 PM 2017-05-25 edited by
- (diff)
- 3:44 PM Ticket #517 (toolshed hide "Model Panel" does not hide model panel) closed by
- fixed: Fixed in 49ca5ec52. The way the "toolshed show/hide" …
- 3:10 PM 2017-05-25 edited by
- (diff)
- 2:10 PM 2017-05-25 created by
- 2:09 PM DeveloperMeetings edited by
- (diff)
- 1:44 PM Ticket #688 (Toolshed 'author' link: TemplateSyntaxError) created by
- On cxtoolshed.rbvi.ucsf.edu, clicking on ISOLDE and then on the author …
- 1:05 PM Ticket #687 (Pick atoms beneath density map surfaces) created by
- On May 25, 2017, at 6:24 AM, Oliver Clarke wrote: Hi, Often I want …
- 12:40 PM Ticket #684 (Bugs in changes.py) closed by
- fixed: Ok, I fixed these 3 problems in atomic/changes.py
- 6:18 AM Ticket #684 (Bugs in changes.py) reopened by
- I see now why I couldn't find it - I was unaware that more than one …
May 24, 2017:
- 4:46 PM Ticket #686 (Provide vector graphics output of silhouette edges) created by
- On May 23, 2017, at 9:50 AM, Oliver Clarke wrote: Hi, Probably low …
- 4:44 PM Ticket #685 (Add wire display style for molecules) created by
- On May 23, 2017, at 9:47 AM, Oliver Clarke wrote: Hi, would it be …
- 10:29 AM Ticket #684 (Bugs in changes.py) closed by
- not a bug: There is a trigger to detect Atom display state changes and many other …
- 3:49 AM Ticket #684 (Bugs in changes.py) created by
- At the moment, the 'model display changed' trigger only fires when an …
May 23, 2017:
- 12:16 PM Ticket #682 (cone geometry) closed by
- fixed
- 12:16 PM Ticket #682 (cone geometry) reopened by
- Fixed. The problem was that the cone base triangles had the wrong …
May 22, 2017:
- 1:53 PM Ticket #682 (cone geometry) closed by
- not a bug: The original code looks correct to me. It is setting the normal …
- 10:06 AM Ticket #681 (Error with partial display of tubes) closed by
- fixed
- 6:54 AM Ticket #683 (atomspec_has_atoms() is inconsistently applied.) created by
- Context: I'm sub-classing AtomicStructure to provide a visualisation …
- 4:17 AM Ticket #682 (cone geometry) created by
- Trivial thing really. In chimerax.core.surface.shapes, line 190, the …
May 19, 2017:
- 5:18 PM Ticket #681 (Error with partial display of tubes) created by
- Error from: open 3jac ~car ~/a:2105-2150 car style model tube …
- 4:09 PM Ticket #678 (Multimodel PDB file crash) closed by
- fixed: Changed PDBio to assign unique model numbers in such cases
- 4:00 PM Ticket #680 (Make deleting Model or Drawing notify parent.) created by
- Want to be able to use m.delete() instead of …
- 3:20 PM Ticket #679 (Crash tab completing pseudobonds collection methods in Python shell) closed by
- fixed: That particular attr is for internal use during session saving and …
May 18, 2017:
- 3:50 PM Ticket #679 (Crash tab completing pseudobonds collection methods in Python shell) created by
- open 3loh # In shell p = session.models.list()[1] # Pseudobond group …
May 17, 2017:
- 7:25 PM Ticket #678 (Multimodel PDB file crash) created by
- Opening the attached multimodel PDB file and then closing all models …
May 16, 2017:
- 4:02 PM Ticket #677 (Problem with file-history session save) closed by
- fixed: Fixed. Oops. File history changes to remember open options broke …
- 3:14 PM Ticket #677 (Problem with file-history session save) created by
- save ~/Desktop/tethers.cxs Session file format is not finalized, and …
- 12:45 PM Ticket #676 (1gmk cartoon strand twist) created by
- Gramicidin has some D-amino acids and in one place the ChimeraX ribbon …
- 12:07 PM Ticket #585 (RFE: add cartoon-style helix tube radius option) closed by
- fixed: Implemented in eff7774.
- 11:57 AM Ticket #675 (Add surface style command) closed by
- fixed: Done. surface style #1 mesh Allowed styles are mesh, dot, solid. …
- 11:57 AM Ticket #675 (Add surface style command) created by
- Add command to change surface style between mesh, dot, solid.
May 15, 2017:
- 5:15 PM Ticket #673 (slanted tube helix 1www /w:5-9) closed by
- fixed: Fixed in d12e9ba. The projection of the atom coordinates …
- 4:12 PM Ticket #551 (cartoon tube "armadillos" in 3jac) closed by
- fixed: In 3jac, residues /b:2112-2148 should really be three short helices. …
- 3:49 PM Ticket #674 (file history enchancement request) closed by
- fixed: Fixed. It now shows the full path to the file or if it is a database …
- 3:11 PM Ticket #674 (file history enchancement request) created by
- Please add a pop up to each tile in the file history showing the …
- 2:43 PM Ticket #650 (Add shutdown to session.triggers) closed by
- fixed: I added an "app quit" trigger invoked before quit closes all windows. …
- 11:55 AM Ticket #475 (crazy tube helices after dssp on 4hhb) closed by
- fixed: Tube selection was not selecting the half-tubes at the end of helices. …
- 10:44 AM Ticket #561 (cartoon should show abutting helices as separate instead of continuous) closed by
- fixed: Adjacent helices now connected by a turn-like one-residue segment in …
- 10:40 AM Ticket #673 (slanted tube helix 1www /w:5-9) created by
- By "slanted" I mean the tube end faces are not normal to the long …
- 10:32 AM Ticket #553 (tube helix with stripes 5cbf) closed by
- fixed: Looks like proper sorting fixed the problem.
- 10:09 AM Ticket #406 (Cartoon for C-alpha only structures) closed by
- fixed: Eric's fix makes 2bml, 1grl and 1www all look correct.
May 13, 2017:
- 11:11 PM Ticket #672 (unable to connect to toolshed?) created by
- Running the daily build on wilkins gives: […] With: […] Since …
May 12, 2017:
- 6:24 PM Ticket #655 (file history format is sticky) closed by
- fixed: File history entries now update when the same file is opened with a …
- 6:22 PM Ticket #646 (consider whether file-history should remember coordset status) closed by
- fixed: Fixed. File history now remembers open command options that have …
- 3:05 PM Ticket #671 (Add symmetric depth cueing) created by
- Begin forwarded message: From: Oliver Clarke <> Subject: Re: …
- 2:58 PM Ticket #670 (Add depth blur effect) created by
- Blur distant objects in the scene to create a sense of depth. This is …
- 1:58 PM Ticket #669 (mmCIF 1grl needs to put missing structure between :302-303) created by
- For each chain in 1grl, the structure changes from fully atomic to …
- 4:23 AM Ticket #668 (Movie encode failure in Linux build) created by
- Simple case of missing library: /home/tic20/apps/chimerax/bin/ffmpeg: …
May 11, 2017:
- 5:52 PM Ticket #667 (Automatically scale maps in volume morph) created by
- Might add a "minRMS true/false" option to the volume morph command to …
- 5:47 PM Ticket #661 (traceback changing surf probe radius after hiding a patch) closed by
- fixed: Fixed. When surface was recalculated it didn't update which triangles …
- 5:20 PM Ticket #666 (Allow user customizable toolbars) created by
- Let the user add toolbar buttons using a command that specifies an …
- 5:10 PM Ticket #665 (Rapid Access improvements) created by
- 1) Tool tips for file names 2) Better icons for non-structures #705 …
- 4:56 PM Ticket #664 (Graphics not redrawn when rapid access hidden) closed by
- fixed: Fixed. Code was not handling expose events. Tested on Linux but not …
- 4:55 PM Ticket #664 (Graphics not redrawn when rapid access hidden) created by
- On Linux and Windows the graphics is not redrawn if the rapid access …
- 4:05 PM Ticket #663 (Tab completion in shell causes crash) closed by
- fixed: Fixed. If there is no active coordinate set because structure has no …
- 4:05 PM Ticket #663 (Tab completion in shell causes crash) created by
- a = AtomicStructure(session) a.<tab> causes crash in shell. Problem …
- 3:12 PM DeveloperMeetings edited by
- (diff)
- 3:12 PM 2017-05-11 created by
- 2:25 PM Ticket #662 (ribbon "normalization error") created by
- When ribbons are computes for 2a06, "normalization error" appears in …
- 10:51 AM Ticket #661 (traceback changing surf probe radius after hiding a patch) created by
- open 2gbp sel zone ligand 6 protein surf sel vis 1 [... ctrl-click to …
May 10, 2017:
- 6:20 PM Ticket #644 (mouse over crosslink ensemble histogram gives IndexError) closed by
- fixed: Fixed.
- 4:28 PM Ticket #645 (mouse over crosslinks histogram of closed structure causes traceback) closed by
- fixed: Fixed.
- 3:43 PM Ticket #652 (infinite loop in PDB reader) closed by
- fixed: Translation of SEQRES records wasn't stripping spaces from residue names.
- 1:55 PM Ticket #660 (Add mouse mode to adjust depth cueing) created by
- Adjust depth cue start/end fractions with mouse mode. Begin forwarded …
- 1:52 PM Ticket #659 (Clip mode shift modifier doesn't work) created by
- The clip mode shift modifier doesn't work because right shift is bound …
- 12:20 PM Ticket #658 (Improve keyboard shortcuts) created by
- Several improvements to keyboard shortcuts would make them more …
- 12:08 PM Ticket #657 (Add RNA feature identification using DSSR) created by
- The DSSR software identifies many basic features of RNA structures. …
May 9, 2017:
- 3:19 PM Ticket #647 (save-restore session compressed two models into one) closed by
- fixed: Fixed -- pseudobond groups weren't saving/restoring their model state. …
- 3:16 PM Ticket #656 (Crop two or more maps to same region) created by
- Begin forwarded message: From: Soumya Govinda Remesh Subject: …
May 8, 2017:
- 3:27 PM Ticket #655 (file history format is sticky) created by
- After opening up a PDB file with format pdb, it stays pdb format …
- 12:23 PM Ticket #654 (Rename crosslinks to "measure lengths") created by
- Might rename crosslinks command to "measure lengths". Begin forwarded …
May 5, 2017:
- 7:45 AM Ticket #653 (Odd library problem installing OpenMM 7.1.0) created by
- As per Tom's suggestion a while back, I've installed OpenMM 7.1.0 into …
May 4, 2017:
- 1:00 PM Ticket #652 (infinite loop in PDB reader) created by
- The PDB reader goes into an infinite loop when trying to open 5a8l. …
May 3, 2017:
- 9:18 AM Ticket #651 (Toolshed failing) created by
- I received errors on submitting a new bundle release (although it does …
May 2, 2017:
- 4:12 AM Ticket #650 (Add shutdown to session.triggers) created by
- At the moment I can't find any way for a Python process to know when …
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