Changes between Initial Version and Version 1 of 2015-2-26


Ignore:
Timestamp:
Feb 26, 2015, 3:05:56 PM (11 years ago)
Author:
Scooter Morris
Comment:

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  • 2015-2-26

    v1 v1  
     1 Attendees =
     2    TomF, TomG, Greg, Eric, Scooter, Elaine
     3
     4= Agenda =
     5 * Work in progress reports for [wiki:2015-2-5 March 2] demo
     6 * Discussion of advisory committee meeting schedule
     7
     8= Discussion =
     9 * Chimera2 Progress Reports
     10  * Eric
     11   * Implemented HTML reply log, including images
     12    * After commands are executed, a thumbnail is shown of what the scene looks like
     13   * Implemented status (status messages now show up)
     14   * Just completed merging of blobs
     15   * Wants to work on "fancier" parts of status logging
     16    * Go away after a period of time
     17    * Keywords (followWith, etc)
     18    * Alignment of status line with command
     19   * HTML window doesn't work very well on Linux
     20  * Greg
     21   * Logging widget does not work on Linux
     22    * WX html demo works but doesn't work on in the context of Chimera2
     23   * Working on side view
     24     * Will eventually support changing camera modes
     25     * Some issues with stereo support
     26     * Currently not working correctly -- side view graphics show up in main window
     27     * Side view is also orthographic rendering, which is not currently supported by Chimera2
     28     * Will work with TomG on this
     29  * TomG
     30   * Oculus Rift on Chimera2: haven't tried, yet.  Will need to do a lot of WX stuff to make it work. Was able to find WX function calls to do the necessary things.
     31   * Did work on supporting cell motion through oculus rift.  Currently you have to jump through a number of hoops.  Tom is working on making this simpler.  Currently, it's pretty fragile, but Tom has been working on making it less fragile.
     32   * Add space navigator port to March 2 list
     33 * Advisory committee meeting 8:30 - 2:00.
     34   * 08:30 Continental Breakfast
     35   * 08:45 Overview of RBVI Activities and Driving Biological Projects
     36   * 09:15 Progress on Technology Research and Development Projects
     37    * Chimera 1 progress (Chimera 1.6 through 1.10, include cellPACK?), 30 minutes
     38     * Web services
     39      * Uniprot
     40      * Loop refinements
     41      * APBS
     42      * Multiple sequence alignments
     43     * Rapid access
     44     * RRDistMaps
     45     * RMF
     46     * Autopack
     47     * Conrad's Crosslinking interface (?)
     48    * Chimera 2 and Large models / EM and WebGL, Oculus, 60 minutes
     49   * 10:45 Break
     50   * 11:00 TR&D Progress Continued
     51    * SFLD, 45 minutes
     52    * Biological context / Cytoscape, 45 minutes
     53   * 12:30 Working Lunch & Group Photo
     54    * Oculus and other demos
     55   * 13:15 Other Center Activities
     56    * Collaborations, service, training, dissemination. 60 minutes.
     57   * 13:45 Committee Business
     58   * 14:00 Adjournment
     59
     60= Notable Chimera1 Features Since Last !AdCo Mtg =
     61(distilled from 1.6-1.10 relnotes by Elaine, see [http://www.rbvi.ucsf.edu/home/meng/docs/relnotes/Chimera1-progress.html single-page combined release notes], possible demo/mention in upcoming meeting)
     62
     63 * as of 1.6:
     64  * Rapid Access interface
     65  * fetch Uniprot protein sequence and annotations
     66  * new ribbon spline options
     67  * improved transparency rendering (single-layer on by default)
     68  * better default model colors (pastel rather than saturated)
     69  * several options for fitting atomic structures into density maps: global search, iterative sequential fitting, symmetric fitting etc.
     70  * Eric: Plot distances/angles/dihedrals for MD trajectories
     71  * Eric: Backgrounds from images or using a color gradient
     72 * as of 1.7
     73  * interactive shadows
     74  * glossy lighting default
     75  * faster loading and graphics
     76  * Animation timeline
     77  * interface to Modeller for building missing segments (RBVI web service or local)
     78  * interfaces to PDB2PQR, APBS, !AutoDock Vina (NBCR web service or local)
     79  * Eric: Significantly improved !PipesAndPlanks tool
     80 * as of 1.8
     81  * show !AutoPack results
     82  * show Rich Molecular Format
     83  * REST interface (RESTServer tool)
     84  * electric field line display for ESP maps (command "measure fieldLines")
     85  * interactive repositioning of 2D arrows
     86 * as of 1.9
     87  * interface to multiple sequence alignment with Clustal Omega or MUSCLE (RBVI web services)
     88  * "struts" command to reinforce structures for 3D printing
     89  * "vseries" volume series playback and processing options
     90  * more efficient save/restore of coordinates in sessions
     91  * export as Collada
     92 * as of 1.10
     93  * protein contact maps color-coded by distance (RR Distance Maps tool)
     94  * fetch PDB biounit, CATH domain
     95  * MDA multidomain assembler
     96  * Modeller interface allows specifying additional distance restraints
     97  * plot all-atom and backbone RMSDs along sequence alignments (previously only alpha-carbon RMSDs)
     98  * show Collada
     99
     100= Next Meeting =
     101 *