Changes between Version 29 and Version 30 of NTTData

Timestamp:

Jun 17, 2021, 6:13:46 PM (4 years ago)

Author:

Tom Goddard

Comment:

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NTTData

@@ -263 +263 @@
 Tom G: Deep SSE Tracer is a machine-learning plugin developed by Jing He. We're interested in developing and interfacing with such machine-learning-related methods. Kristen: some are better than others, certainly. TG: CryoDRGN identifies multiple conformations in EM data. TG: we are also looking at using dimensionality-reduction approaches. In VR can reduce to 3D. Elaine: could think also about animating through time, using colors/sizes as additional dimensions, etc.
 
-Kristen: question about exporting glb of an assembly of 6htx, gives an error. "index 1 is out of bounds" TG: it's a bug. Possible workaround is to use "sym" with "copies true" (requires more memory), but we should also fix the bug. The glb file could us instancing, but we are not writing it that way currently. Greg: should write glb with instancing. TG: yes, maybe as an option, but make it the default.
+Kristen: question about exporting glb of an assembly of 6htx, gives an error. "index 1 is out of bounds" TG: it's a bug. Possible workaround is to use "sym" with "copies true" (requires more memory), but we should also fix the bug. The glb file could use instancing, but we are not writing it that way currently. Greg: should write glb with instancing. TG: yes, maybe as an option, but make it the default.
 
 Phil: 
@@ -271 +271 @@
 - Re export: PDB doesn't have total molecular weight, only per each entity. We remove waters and other stuff but would like export to include total molecular weight of atoms that are present (not including hydrogens or missing segments). Elaine: why not atom count instead? Darrell: let's re-examine the logic and then take a look at calculating what we need. Darrell: important thing is really the scale. TG: like dimensions in angstroms? Darrell: degree of magnification. Elaine: inherently angstroms, but we don't know how large it will be when 3D-printed. Greg: Blender units are meters. Phil: perhaps useful to export lengths of bounding box in X,Y,Z. Greg: we may need to improve our calculation of the global bounding box. Darrell: also may be rotated relative to the molecule.  Elaine: how about '''measure inertia'''?  But problem is that it doesn't enclose everything like a convex hull.  Tom G: perhaps we can provide a similar command that encloses all atoms and/or surfaces. Phil: maybe we could use the ellipsoid to reorient the model along screen X,Y,Z. Tom G: maybe we can add the ability to ChimeraX to dump a separate XML or JSON file with the metadata instead of stuffing it all into the GLTF.
 
-Philip: ...some discussion Elaine didn't understand... Greg: we need to add startup option to avoid phoning home. TomG: should do more things, also avoid reading/writing user data and settings. Eric: what about caching fetch data?
-
+Philip: Want to run ChimeraX without accumulating history in a home directory, and also without contacting RBVI Toolshed server every fresh start. Greg: we need to add startup option to avoid phoning home. Also can make a temporary directory and set HOME environment variable to that directory so fetched files, file history, ... goes to that directory.  TomG: should do more things with a "stateless" option, avoid reading/writing user data and settings. Eric: what about caching fetch data in ~/Downloads in stateless mode?  TomG: Yeah, that is a problem.
+