| | 1 | = Attendees = |
| | 2 | |
| | 3 | Elaine, Eric, Greg, Conrad, TomG, TomF |
| | 4 | |
| | 5 | = Agenda = |
| | 6 | * Review action items from last meeting |
| | 7 | * Chimera 1.11.2 release |
| | 8 | * ChimeraX issues |
| | 9 | * Metadata for tools/bundles |
| | 10 | * Assign required site-visit functionality to people |
| | 11 | * Discussion of site visit scenarios |
| | 12 | * Continuation of 8-29 discussion |
| | 13 | |
| | 14 | = Discussion = |
| | 15 | * Previous action items: |
| | 16 | * None |
| | 17 | * Chimera 1.11.2 release |
| | 18 | * Eric got new rotamer library, defer to later release |
| | 19 | * Many Sierra problems with touchpad and/or scrolling |
| | 20 | - ~~Take a look at JDK fix for scrolling problem (Scooter will forward to TomG) |
| | 21 | - Conrad will bring laptop in on Monday to show IDLE crash in same place |
| | 22 | - Defer release in hopes of fixing this bug first |
| | 23 | - TomG will ask Briana(?) to test 1.10 for crashes |
| | 24 | * ChimeraX issues |
| | 25 | * Ribbon progress |
| | 26 | * Lots of stuff on Elaine's [http://www.cgl.ucsf.edu/home/meng/chimera2/user/commands/cartoon3.html documentation page ] |
| | 27 | * Conrad will check out nucleosome ribbon display |
| | 28 | * Metadata for tools/bundles |
| | 29 | * Change in tool/bundle template |
| | 30 | * For UI purposes, there is no API for GUI options in open or save panel for bundles for now |
| | 31 | * For extra open/save arguments, register them in custom initialization function |
| | 32 | * Steps in updating to new metadata |
| | 33 | 1. ~~Rename "tools" to "bundles", "gui.py" to "tool.py" |
| | 34 | 2. Add support for new metadata format in toolshed |
| | 35 | - ~~Include backwards compatibility with bundles with old metadata style code |
| | 36 | - Including refactoring "fetch" code |
| | 37 | - Initialization order should be based on dependency |
| | 38 | 3. Migrate limited set of bundles to test new code |
| | 39 | 4. Migrate remaining bundles |
| | 40 | 5. Delete code for old metadata |
| | 41 | * New toolshed core functionality |
| | 42 | * New deliverables: selectors, mouse modes, ~~command line options (low priority)~~ |
| | 43 | * ~~Add --cmd option to execute ChimeraX command from command line: |
| | 44 | {{{ |
| | 45 | chimerax --cmd "ts load RESTServer; rest start" |
| | 46 | }}} |
| | 47 | * Make main startup code a bundle to be called from shim code |
| | 48 | * Undeletable bundles |
| | 49 | * New toolshed UI |
| | 50 | * Tabbed interface for installed bundles and all bundles |
| | 51 | * Both will provide interface to search/browse by deliverables (tools, commands, file formats, selectors, etc) |
| | 52 | * Perhaps a separate "Active Tools" tool |
| | 53 | * Toolshed "server" |
| | 54 | * Need to implement wheel upload to update app store database and display |
| | 55 | - Define where resources are found in wheels, e.g., metadata, icon, screenshot, etc. |
| | 56 | * Prototype MAV displays sequence/alignment in a Qt window |
| | 57 | * Structure-sequence association works but no user visible effects |
| | 58 | * IHM format support |
| | 59 | * TomG met with SJ and Ilan about nup82 (not promising) |
| | 60 | - Data is all in SJ's personal Dropbox folder and need to be uploaded to (private) github |
| | 61 | - SJ has no time to work on it this week |
| | 62 | - A lot of data is missing (sequence alignment, localization densities, unaligned ensembles) or poorly formatted (e.g., ENDMOL instead of ENDMDL) |
| | 63 | * OpenMM is installed |
| | 64 | * Tristan Croll, MDFF author, is testing out ChimeraX |
| | 65 | * Croll is working with Peter Eastman on OpenMM bug |
| | 66 | * Also testing out Chai3D haptics toolkit and Falcon device |
| | 67 | * Croll mentioned that people were impressed by ChimeraX at CCPEM |
| | 68 | * Assign required site-visit functionality to people |
| | 69 | * Cytoscape and REST interface (Conrad, Scooter) |
| | 70 | - rest_server bundle is committed |
| | 71 | - list_info bundle is under way |
| | 72 | - need simplified "findclash" command |
| | 73 | * ~~Side view on !PyQt (Greg) |
| | 74 | * Toolshed server side (Conrad) |
| | 75 | - CyAppStore running on https://cxtoolshed.rbvi.ucsf.edu |
| | 76 | - need wheel uploading |
| | 77 | * Toolshed client side (Greg) |
| | 78 | * Ribbons (Conrad) |
| | 79 | * IHM cross-link distribution histograms (TomG) |
| | 80 | - Interest from SJ and Ilan |
| | 81 | * Interface viewer (TomG) |
| | 82 | - Add selection outlines on 2D plot from 3D selection |
| | 83 | * IHM mmCIF support (TomG) |
| | 84 | * MAV (Eric) |
| | 85 | * blastpdb (Conrad) |
| | 86 | * Reach goals |
| | 87 | * String database (Scooter, Conrad) |
| | 88 | * Hydrogen bonds and contacts (Eric) |
| | 89 | * Link to NGL, !LiteMol (Scooter, Conrad, Greg) |
| | 90 | * Molprobity on Opal (Scooter) |
| | 91 | * Domains |
| | 92 | * Web service, Uniprot? (Eric) |
| | 93 | * Integration into hierarchy (Eric) |
| | 94 | * Interactive 2D graph (team) |
| | 95 | * Hierarchy browser |
| | 96 | * UI cleanup (team) |
| | 97 | * Site visit |
| | 98 | * Plan on three ~~or four~~ shorter DBP-based "vignettes" instead of two longer scenarios |
| | 99 | * Vignette with presenters: |
| | 100 | - '''Sali''' and IHM |
| | 101 | - '''van den Bedem''' and contact networks |
| | 102 | - '''Horwitz''' and '''Johnson''' and optical microscopy |
| | 103 | - Krogan? |
| | 104 | - deRisi student? |
| | 105 | - Chiu? |
| | 106 | - Developer testimonial from ''Tristan'' |
| | 107 | * Allot time for Chimera 1 if site visitors are not familiar with Chimera 1 |
| | 108 | - Waiting for committee member list |
| | 109 | * Continuation of 8-29 discussion |
| | 110 | |
| | 111 | = Outstanding Action Items = |
| | 112 | * None |
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
