Changes between Version 4 and Version 5 of NIAID2023


Ignore:
Timestamp:
May 25, 2023, 2:03:08 PM (2 years ago)
Author:
Elaine Meng
Comment:

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  • NIAID2023

    v4 v5  
    4343== 5/25/2023 ==
    4444
    45 Phil, Darrell, Kristen Browne, Andi Bueckle; Scooter, Zach, Selina, TomG, Eric, Elaine
     45Phil, Darrell, Kristen Browne, Andi Bueckle; Scooter, Zach, Selina Liu, TomG, Eric, Elaine
    4646
    4747Scooter describes Alex Pico's recent Wikipathways work
    … …  
    5252
    5353Another issue was higher-resolution surfaces from Chimera than ChimeraX. Phil made a table comparing # vertices etc. for several example structures of different sizes, we're not sure why there are so many more triangles from the NIH3D pipeline than in ChimeraX directly. Maybe the sharp boundaries parameter?  None of their colorings are per atom, only per chain, by ESP, or by MLP. So they could turn that option off (sharpBoundaries false).
     54[I saved an image of his table but couldn't figure out how to insert it here]
    5455
    5556Phil didn't get a chance to look at the pseudobonds-not-connecting issue.
    … …  
    5758Andi's writing up something but it's not yet ready for discussion.
    5859
    59 TomG: maybe the study should use the standalone VR approach with Quest 2.  Andi: is this available as a build?  He will take a look at [https://www.rbvi.ucsf.edu/chimerax/data/looksee-mar2023/looksee.html Tom's demo]
     60TomG: maybe the study should use the standalone VR approach with Quest 2.  Andi: is this available as a build? TomG: Yes. Take a look at ChimeraX presentations on this, e.g. [https://www.rbvi.ucsf.edu/chimerax/data/looksee-mar2023/looksee.html demo1] [https://www.rbvi.ucsf.edu/chimerax/data/paxlovid-vr-mar2023/paxlovid.html demo2] [https://www.rbvi.ucsf.edu/chimerax/data/vr-plans-may2023/vr_plans.html demo3]
     61
     62Scooter introduces Selina
     63
     64Scooter says the contract was adjusted down for the 2 months time lost
     65
     66Phil: back to VR, one of the structural biology groups here is asking for headset recommendations.  Tethered HP (Windows mixed reality?) seems robust but controller buttons are quite different and not recognized by ChimeraX currently. The worst is that that one that brings up the menu is not recognized.  TomG: we have Windows mixed reality setup and it was working, but I haven't used it for a few years, maybe API changed somehow and/or you have a different version.  Phil: positions of the buttons don't map correctly, both A and B depress same thing on virtual representation, thumbstick and menu button not recognized at all.  Only grip and trigger and A/B (melded) are recognized.
     67
     68TomG: I'll try our Windows mixed reality and get back to you.
     69
     70Phil: obvious recommendation would be RiftS except we can't get those anymore, whereas one can still get HP Reverbs.  TomG: this group already has the expensive PC? Phil: yes.  Andi: we have the tracking stations on tripods, which makes them easy to move around.
     71
     72TomG: We hope to get ChimeraX working with OpenXR, so it wouldn't be dependent on SteamVR.
     73
     74TomG: I found that devices couldn't "see" each other on guest wifi, only the secure one.  This may be an issue for other institutions.  Phil: We are still working through wifi issues in the bioviz lab, headsets need 80mHz and router is not providing that.  Andi: too hard fighting with institutional IT, I just have to use cables everywhere.  Phil: Meghan is doing a great job coordinating the hardware setups here.
     75
     76Discussion of airlink connections.
    6077
    6178== 5/11/2023 ==