Changes between Version 23 and Version 24 of NIAID2024

Timestamp:

Aug 29, 2024, 1:54:39 PM (14 months ago)

Author:

Elaine Meng

Comment:

--

NIAID2024

@@ -83 +83 @@
 == Meeting Minutes ==
 
+== 9/26/24 ==
+
+== 9/12/24 ==
+
+Phil and Meghan in Africa, Scooter on vacation. Tentatively schedule Zoom time to make sure the NIH3D changes are done, can cancel if resolved earlier by email.
+
 == 8/29/24 ==
 
-Eric, Elaine, Zach, Piet, Scooter; Phil, Meghan, Mike, Kristen
+Tom, Eric, Elaine, Zach, Piet, Scooter; Phil, Meghan, Mike, Kristen
 
 Phil: our senior leadership came in this week, they work with several structural biology centers. We were impressed that he could lead a VR ChimeraX session showing an AIDS drug. It went quite well except for the trying to prevent the tethers of the four people from getting tangled up. Our wifi is in flux so we had to use the cables.
@@ -91 +97 @@
 Scooter: is there a grant opportunity with those higher-ups?  Phil: possibly but no specific knowledge.  Scooter: we are considering R24 mechanism vs. or in addition to R01, so it would be helpful to build connections to any receptive parties.  Phil: they want to get ChimeraX VR in all of the structural biology centers.  Will see if that can lead to funding opportunities.
 
-Phil: They plan to use ChimeraX VR in their retreat Sept 18. 10 headsets at once.  One difficulty is how to position the model for so many participants, any thoughts?  Tom: with interactive ChimeraX (not LookSee)?  Phil: Yes.  Tom: how do you draw the boundary?  If SteamVR, everybody should see the model floating in the same place in the room. If there is a rectangle rather than square, it considers the viewer as facing a long side, and the order of drawing the four boundaries matters. Phil: does the size matter?  Tom: maybe not, but people would need to specify the same center.  With Oculus Metalink, not sure how it would work.  Phil, Meghan: we'll be in Africa most of the month and not much time to work on setup.  Only Sept 16-17.  We plan to have the 10 people seated and not move around much. Maybe we'll make the area small, like 2x2 meters. Phil: if we draw the boundary with the user in middle, where would the model be placed? Tom: in the middle, so it would be right on top of the user. Tom: I've thought about having a separate small box for each user, not intersecting, but that may not be good for following a presenter that is farther away.
+Phil: They plan to use ChimeraX VR in their retreat Sept 18. 10 headsets at once.  One difficulty is how to position the model for so many participants, any thoughts?  Tom: with interactive ChimeraX (not !LookSee)?  Phil: Yes.  Tom: how do you draw the boundary?  If SteamVR, everybody should see the model floating in the same place in the room. If there is a rectangle rather than square, it considers the viewer as facing a long side, and the order of drawing the four boundaries matters. Phil: does the size matter?  Tom: maybe not, but people would need to specify the same center.  With Oculus Metalink, not sure how it would work.  Phil, Meghan: we'll be in Africa most of the month and not much time to work on setup.  Only Sept 16-17.  We plan to have the 10 people seated and not move around much. Maybe we'll make the area small, like 2x2 meters. Phil: if we draw the boundary with the user in middle, where would the model be placed? Tom: in the middle, so it would be right on top of the user. Tom: I've thought about having a separate small box for each user, not intersecting, but that may not be good for following a presenter that is farther away.
 
 Meghan: somebody's virtual head was blocking somebody else's view.  Certainly for a large number of people at the retreat, we should turn off the virtual head images. Tom: each person would need to turn it off for themselves, the way it looks currently.
@@ -99 +105 @@
 Phil: what if everybody is trying to look from the same vantage point at the same time?  Like down a pore. Tom: would need to use either common coordinate system but with pass-through video so you don't bump into each other, or separate coordinate systems with non-overlapping boundaries.  
 
-Tom: at least LookSee has a built-in method to align coordinate systems, and you don't have to worry about tethering.
+Tom: at least !LookSee has a built-in method to align coordinate systems, and you don't have to worry about tethering. People would still have to take turns if they need to see from exactly the same vantage point when their coordinate systems are aligned. Phil: I'll be typing ChimeraX commands for interactive VR. Tom: you can make multiple models for LookSee ahead of time and switch between them.  Phil: I've tried that aproach too.
+
+Meghan: the tethers must go but we won't be able to do it before the 18th, unfortunately.
+
+Phil: got very bad skyline effect trying to use passthrough at home (tethered), but it might be my home laptop.  Haven't tried in the bioviz lab 4000 series yet.  Tom: passthrough with tether was working fine for me on both 3000 and 4000 series. Try in the lab.  If problems, may require more troubleshooting.
+
+Scooter: let's let Kristen ask her question.  Kristen: Bhinnata wants to know where Eric is on the alphafold pipeline options since we have a release in first week of October.  Eric: stuck because it's unclear in which cases output should be omitted. All vs. high-conf, each has several kinds of coloring.  Drop outputs in <17 high-conf residues in largest contiguous piece, but these are different for surface vs. ribbon. Phil: separate tests for ribbons and surfaces. If ribbon big enough, output all  relevant colorings of ribbons. If surface big enough, output all colorings of surfaces.  Eric: given that information, should be a week or two to get it done.
+
+Phil: the good news is that our test outputs from the current presets look great!
 
 == 8/15/24 ==