Changes between Version 45 and Version 46 of NeteSOW

Timestamp:

Nov 19, 2020, 1:44:11 PM (5 years ago)

Author:

Elaine Meng

Comment:

--

NeteSOW

@@ -211 +211 @@
 3D Pipeline:
 
-- Eric modified the ChimeraX pipeline script to allow specifying which branch to take (small mol, macromol, or map), or if not specified then chosen automatically.  Regardless, the script reports what branch is used.  He put the script on your github about a week ago... any feedback?
+- Eric modified the ChimeraX pipeline script to allow specifying which branch to take (small mol, macromol, or map), or if not specified then chosen automatically.  Regardless, the script reports what branch is used.  He put the script on your github several days ago.  Feedback?
 
 - Eric is working on porting addcharge to ChimeraX for a more complete implementation of coloring by Coulombic ESP
@@ -228 +228 @@
 
 - Our NIH 3D and VR meeting contract goals have made good progress.  Which one of the 3 other areas, segmentation, medical imaging and HuBMAP would be best to get started?  Are there BCBB projects we could assist on in these 3 areas? 
+
+
+** Discussion **
+
+3D Pipeline:
+- Phil has tried the script, seems to work well in a few tests, needs to try with more data including edge cases and wide range of sizes
+
+- The script looks for a recommended contour level for maps from EMDB, but some maps do not have this annotation
+
+- They will need Chimera 1.15 because of changes in RCSB PDB fetch
+
+- Add new fetches?
+  - Crystallography Open Database provides CIF, but ChimeraX does not read small-molecule CIF
+  - ZINC provides formats ChimeraX reads, we will reach out to Shoichet and/or Irwin
+
+VR Meetings:
+- Meghan: we will try a VR meeting with Uganda
+- Victor: ...or with our own low-bandwidth machine
+- the Meeting GUI will be very helpful
+- TomG will investigate lowering the bandwidth requirement by using Messagepack