Changes between Version 4 and Version 5 of MSC2019Deliverables

Timestamp:

Oct 24, 2019, 1:52:05 PM (6 years ago)

Author:

Elaine Meng

Comment:

--

MSC2019Deliverables

@@ -31 +31 @@
   i. cryoEM modeling -- rotamers, structure building and verification, minimization
     - ISOLDE integration with VR
-    - [[span(style=color: #00AA00, 'swapaa' command implemented.  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 )]]
-      1. [[span(style=color: #00AA00, Refactored rotamer library handling so that the libraries are provided by separate bundles and therefore new rotamer libraries could be supplied by third parties via the Toolshed )]]
   - User interface improvements: better menus and UI appearance
  b. Measure and display distance between two specified points in space in VR, both molecular models and medical images.
@@ -51 +48 @@
  B. Instructional Material and tools documentation (Elaine 609 hours)
   a. Detailed instructions for all features shall be provided in a user manual.
+[http://rbvi.ucsf.edu/chimerax/docs/user/index.html ChimeraX User Guide at the RBVI website] **note to Scooter** because viewdockx was used as the test for the future documentation reorganization, the links to ViewDockX tool and command help are broken in this website copy. The downloaded User Guide shown from ChimeraX help menu does not have this issue.
   a. Written user guides and tutorials shall be available as an HTML page and/or a downloadable PDF.
+[http://www.rbvi.ucsf.edu/chimerax/tutorials.html ChimeraX tutorials index ]
+...includes [https://www.rbvi.ucsf.edu/chimerax/data/rml-sep2019/synuclein.html Alpha-synuclein fibrils ChimeraX tutorial for Rocky Mountain Laboratories workshop. September 2019.] and
+[https://www.rbvi.ucsf.edu/chimerax/data/rml-sep2019/proteasomes.html EM tomography ChimeraX tutorial looking at proteasomes around aggregated fibrils in neurons for Rocky Mountain Laboratories workshop. September 2019.] 
 5. Project planning, administration, and reporting (Tom 87 hours, Scooter 174 hours)
   a. A project schedule, implementation plan, and documentation plan will be provided.
@@ -57 +58 @@
 6. Other related developments
   - Exploratorium demonstration
+[https://www.exploratorium.edu/visit/calendar/after-dark-october-24-2019 Exploratorium After Dark Party, October 24, 6-10 pm. ChimeraX VR will be used to show programmed cells form 3D structures. Data from Wendell Lim's lab; the cells are genetically engineered to self-organize by signaling and adhesion.]
   - Makers Lab demonstration
+[https://calendars.library.ucsf.edu/event/5961014 ChimeraX used for a virtual reality look at molecules, cells, and tissues in the UCSF Library Makers Lab, Parnassus Campus, noon-1pm November 15.2019.]
   - UCSF news article highlighting ChimeraX VR and drug resistance
+[https://pharmacy.ucsf.edu/news/2019/10/vr-drug-discovery-makes-precision-therapy-reality VR Drug Discovery Makes Precision Therapy a Reality] and
+[https://youtu.be/S4lDzUEUFL0 video from article on YouTube]