Changes between Version 27 and Version 28 of NeteSOW

Timestamp:

Oct 22, 2020, 2:03:31 PM (5 years ago)

Author:

Elaine Meng

Comment:

--

NeteSOW

@@ -113 +113 @@
 == 10/22/2020 ==
 
-Topics
-- Scooter on vacation for a month, sailing home from Mexico, returns Nov 22.
+Darrell, Meghan, Phil, Philip, Kristen, Victor; Greg, Elaine, Eric, TomG
 
-- What topics would NIAID like to discuss today?
+Topics: 
+- Scooter on vacation for a month, sailing home from Mexico, returns Nov 22 (Elaine: this is approximate, weather-dependent)
+ 
+- NIH 3D pipeline
 
-- NIH 3D pipeline
- - Improved JSON error handling, Eric Pettersen
  - Will convert 3D Print Exchange scripts to ChimeraX
-  - Got  scripts from Phil Cruz
-  - Joined GitHub repository for scripts setup by Philip Macmenamin, 2-factor authentication
+  - Joined GitHub repository for scripts setup by Philip Macmenamin, 2-factor authentication; seems that 2FA wil not be a problem for our day-to-day work
+  - Got 3 scripts from Phil Cruz
+  - Eric: the 2 shorter scripts are in good shape, few issues:
+    - ChimeraX does not write VRML; not absolute requirement, can convert glb to vrml in separate step
+    - ChimeraX "graphics quality" can be used to adjust numbers of triangles for STL output
+    - no incremental radius adjustment a la Chimera vdwdefine plus/minus; Eric will supply python to do this 
+    - no combine, why was it used?  Phil: to handle biological assemblies that were multiple models.  Eric: now the fetch gets the assemblies as single models
+  - Philip asks about taking all the file reading and branching out of the ChimeraX scripts and instead have several separate ChimeraX scripts that are called; however, parsing with ChimeraX has several advantages
+  - Phil: actually may want to combine small-molecule and macromolecule scripts into one to reduce user error; distinction is presence of "standard residues" (biopolymer chains)
+  - Darrell: how about also combining with volume script, have ChimeraX identify if upload is map?  Eric: should be doable, at least if filename has standard suffix
+  - Darrell: will also need to distinguish which database goes with an identifier for fetch purposes
+  - Phil: if REST, is a hybrid approach possible? 
+ - Eric improved error reporting in JSON
 
+Potential topics not covered: 
 - VR meetings: firewalls, slow networks, 3 or 4 participants
  - Wrote documentation for setting up AWS server added to meeting command web page
- - David Liou has setup NIAID AWS server, will test tomorrow
+ - David Liou has set up NIAID AWS server, will test tomorrow
  - Working on improved handling of low-bandwidth connections
  - Adding meeting command proxy options for simpler use of AWS
 
-Meeting notes
-
-Darrell, Meghan, Phil, Philip, Kristen, Victor; Greg, Elaine, Eric, TomG