Changes between Version 13 and Version 14 of MSC2019Deliverables

Timestamp:

Oct 25, 2019, 1:44:44 PM (6 years ago)

Author:

Tom Goddard

Comment:

--

MSC2019Deliverables

@@ -30 +30 @@
   i. medical imaging
   i. cryoEM modeling -- rotamers, structure building and verification, minimization
-    - [[span(style=color: #00AA00, ISOLDE integration with VR - initial test for feasibility )]]
     - [[span(style=color: #00AA00, 'swapaa' command implemented.[http://rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html documentation]  Largely a port of Chimera code, with the principal differences being: )]]
         1. [[span(style=color: #00AA00, New code to handle the fact that Chimera treats alternate locations as separate atoms whereas ChimeraX treats them as a single atom. )]]
@@ -38 +37 @@
       1. [[span(style=color: #00AA00, Configurable and embeddable H-bonds GUI so that the Rotamers tool can add an H-bonds column to the rotamers table.  As a "side effect" an H-bonds tool was implemented.[http://www.cgl.ucsf.edu/chimerax/docs/user/tools/hbonds.html documentation] )]]
       1. [[span(style=color: #00AA00, Similar to the previous point, a configurable and embeddable clashes/contacts GUI needs to be ported/implemented.  This will be the last major piece of the Rotamers tool.  When completed, both embeddable GUIs will also be incorporated into the ViewDockX tool.)]]
-  - [[span(style=color: #00AA00, User interface improvements: menus and popup windows in VR, every tool is its own movable and closable panel, custom Oculus controller button depiction,  Oculus thumbstick modes for zoom, rotate, others... )]]
+    - [[span(style=color: #00AA00, ISOLDE refining atomic models in cryoEM maps, initial test for feasibility for using with VR. )]]
+    - [[span(style=color: #00AA00, Segger EM segmenttion tool ported to ChimeraX. GUI can be used in VR. )]]
+    - [[span(style=color: #00AA00, Created EM map fitting GUI - can be used in VR. )]]
+    - [[span(style=color: #00AA00, Volume Eraser GUI and VR mode added. )]]
+    - [[span(style=color: #00AA00, GUI color and size controls for markers placed on maps . )]]
+  - [[span(style=color: #00AA00, General VR user interface improvements. )]]
+    1. [[span(style=color: #00AA00, Menus and popup windows now supported in VR. )]]
+    1. [[span(style=color: #00AA00, Every tool is its own movable, resizable and closable panel. )]]
+    1. [[span(style=color: #00AA00, Improved zooming to avoid models receding in distance. )]]
+    1. [[span(style=color: #00AA00,  Oculus controller button layout. )]]
+    1. [[span(style=color: #00AA00,   Oculus thumbstick modes for zoom, rotate, map series. )]]
  b. Measure and display distance between two specified points in space in VR, both molecular models and medical images.
   - [http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#tapemeasure Tape measure VR and mouse mode added.  For maps only currently.]
@@ -48 +57 @@
 3. Support for multiuser sessions in a virtual reality environment (Tom 87 hours, Eric 174 hours, Conrad 435 hours)
  a. The application will allow multiple ChimeraX users to enter a shared session to interact with a 3D representation of the data in virtual reality (scene sharing)
+    - [[span(style=color: #00AA00, Acquired and tested newly released VR headset Oculus Rift S in multiperson VR sessions. )]]
  a. An ideal solution will allow users from both ends (remote, or in the same physical room) to start meetings on demand and to connect without opening firewalls.
 4. Outreach
  A. Workshops, Training and presentations (Tom 164 hours, Elaine 87 hours)
   a. If available, the subcontractor shall attend a meeting at NIAID’s Rocky Mountain Labs location in Hamilton, Montana. This is tentatively scheduled for August 5-9, 2019, as part of a NIAID/OCICB site visit to showcase virtual reality technology for scientific data visualization to support NIAID research.
-    - [[span(style=color: #00AA00, Tom G attended workshop, presented ChimeraX cryoEM training, many VR demos, several new ChimeraX VR features requested by Rocky Mt people implemented (menu support, Oculus thumbstick controls) )]]
+    - [[span(style=color: #00AA00, Tom G attended workshop, presented two ChimeraX cryoEM training [https://www.rbvi.ucsf.edu/chimerax/tutorials.html tutorials], many VR demos, followed up implementing new ChimeraX VR features requested by Rocky Mt people (menu support, Oculus thumbstick controls, function key support) )]]
   b. The subcontractor may propose one or more additional conference events relevant to the work, at which they will showcase the application in an oral presentation and/or hands-on conference exhibit or training. Justification shall be provided for how this will benefit NIAID.
+    - [[span(style=color: #00AA00, Tom G gave cryoEM ChimeraX tutorial at Stanford cryoEM workshop, organized by Wah Chiu, head of National Center for Macromolecular Imaging, gave VR demos looking at cryoEM and atomic models ATP synthase. )]]
+    - [[span(style=color: #00AA00, Tom Ferrin gave [https://www.rbvi.ucsf.edu/chimerax/data/acs-aug2019/drugvr.html talk] on molecular VR at the ACS annual meeting including video of multiperson VR use. )]]
   c. A virtual help desk for users
     - [http://www.rbvi.ucsf.edu/pipermail/chimerax-users/index.html chimerax-users archive]
+    - [[span(style=color: #00AA00, Email discussions assisting multiple users in purchasing suitable VR headsets and computers for use with ChimeraX. )]]
  B. Instructional Material and tools documentation (Elaine 609 hours)
   a. Detailed instructions for all features shall be provided in a user manual.