Changes between Version 8 and Version 9 of NIAID2023

Timestamp:

Jun 15, 2023, 2:06:01 PM (2 years ago)

Author:

Elaine Meng

Comment:

--

NIAID2023

@@ -55 +55 @@
 Phil: to me, long calculations are OK as along as the user's expectations are managed.  Darrell: I agree, the expectations for a website like NIH3D can be different than for an interactive program like ChimeraX.  Still, we don't want ridiculously huge files that many will not be able to handle. Kristen: in situations where we have to re-run everything, multiday calculations are less feasible.  May also need to warn users specifically that processing will take a long time, and have some kind of indicator to us as pipeline developers that the process is still running/proceeding rather than hung.
 
-Kristen: can we change these parameters?  Elaine: they are command options. Phil: I see the preset-generated commands and then make variations on those commands and try them.
+Elaine: the hard part is the nitty gritty of setting the rules and boundaries. Darrell: 
+
+Kristen: can we change these parameters?  Elaine: they are command options. Phil: I see the preset-generated commands and then make variations on those commands and try them. TomG: I would edit the python in the bundle files. Try it on a set of test cases and evaluate the results.  Eric: we should address the problem systems, make sure the appropriate grid size is used (wrong sizes found by Phil), have Kristen apply decimation and see the results, see if TomG can speed up surface calculation, and decide on sharpBoundaries true or false.  Phil: advantage to false is smaller files.  Eric: maybe true for visualization presets, false for printing presets.  Kristen: I should take a look at decimation for both sharp true and sharp false, see what happens to those boundaries.
+
+Phil: we're only talking about surfaces so far.  I also want to think more about ribbon cross-section (number of sides, etc.). 
+
+Discussion of lighting ("smoothing" using surface normals). Kristen: should we show the smoothing in the viewer, or is that misleading when the model will be printed?  Similarly, what if model is too big for VR use? How to manage expectations and give the right level of detail for the intended use?  Darrell: we should discuss amongst ourselves outside of this meeting with the UCSF folks. TomG: that mammoth example was interesting, giving some choices for level of resolution, but that site did not give file sizes, which was problematic.  People need to understand what they are getting, to avoid frustration.  Darrell: maybe we could offer a printable version and a VR-ready version.  Eric: In most cases we do offer two versions, or at least specific settings suitable for printing. I'm thinking sharpboundaries true except for the larger printable models.
+
+Phil: for testing, could you make an additional set of presets same as existing except with opposite sharpBoundaries settings?  Can send wheels directly instead of putting on toolshed.  Where are the presets loaded?  Eric: use command "info path"... Phil: found it. TomG: after editing, restart ChimeraX.
+
+Phil: do you have a feel for maximum triangles for VR? TomG: Quest2 or QuestPro 900,000 without passthrough, 700,00 with passthrough.  Higher-end card 20 million triangles. Kristen: I want to make scenes with lots of proteins.  TomG: I'll send you a link about somebody who was making spectacular multiprotein scenes.
 
 == 6/8/2023 ==