| 91 | | notes |
| | 91 | Some discussion of Andi's scary (almost-real-looking) avatar since he is Zooming using the Vision Pro. The varying amounts of transparency and the unrealistic mouth movements are the giveaway. |
| | 92 | |
| | 93 | Phil: Kristen had an interesting idea to output files for Mesoscape. Scooter: I talked to some people at VIZBI... planning a collaboration for publishing data to Schol-AR; the developer (Tyler) happens to also be a radiologist and may be helpful in evaluating our medical image stuff. Discussed maybe having a ChimeraX REST interface to publish to Schol-AR. Kristen and Phil: we may be interested in adding a connection to Schol-AR from NIH3D. |
| | 94 | |
| | 95 | Scooter: Eric has a present for you, especially Darrell. (Zoom technical difficulties, disconnected, reconnected.) Eric demonstrates worms, everybody is enthusiastic. Darrell: would be fun to try 3D printing. Might need struts. Kristen: is this in other programs? Elaine: yes, Pymol, Chimera, etc. Phil: re NIH3D I also wanted to discuss the quick-submit workflows for alphafold... we need to decide which are the standard outputs: pLDDT and PAE domain coloring, ribbons and surfaces, maybe hide low-pLDDT parts? Transparency? Elaine: pLDDT coloring shows low confidence as red, or it could be gray in combination with PAE domain coloring. In ChimeraX you can specify all residues with bfactor (pLDDT is in the bfactor field) greater than some value. |
| | 96 | |
| | 97 | Scooter: this all ties into what metadata we want to have in the GLTF output. Groups of residues predefined, e.g. "high pLDDT" or by chain ID or domain, etc. Phil: Darrell, maybe you can help us decide on the standard set of outputs. Darrell: should be useful and include ones that are harder for some people to generate on their own, which used to be the case for ESP coloring. We'll have to put our heads together and decide on an edited set. Kristen: maybe we could offer checkbox choices of which outputs the user wants. |
| | 98 | |
| | 99 | Phil: ChimeraX gltf outputs look washed out when embedded into Microsoft documents (Powerpoint and Word). Due to their oversaturated lighting model, which is unlikely to be addressed by Microsoft, so we have to try to work around it. I can generate ChimeraX gltf files that look better after embedding in such documents by using different settings in ChimeraX (I have my own preset for this, which uses "color modify" to lighten the colors) but that may require yet another set of output options. Kristen: I hacked Powerpoint to get around it but it's not trivial. See this in the forum for the Microsoft lighting: https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-inside-powerpoint/d0c0c316-8019-4c25-b0f6-86500e512f91 |
| | 100 | |
| | 101 | Meghan posted another link in the chat |
| | 102 | https://answers.microsoft.com/en-us/msoffice/forum/all/powerpoint-uses-gltf-but-doesnt-support/002d1f4e-061d-4ab6-a692-ed217945724a |
| | 103 | |
| | 104 | Meghan: are there ways to fix the gltf after it's output? Blender, but having to download Blender is another barrier. Kristen: maybe NIH3D could have a "optimize gltf for Microsoft documents" service that runs our own Blender. Phil, Darrell: it may be a useful utility. Darrell: does gltf outputs from ChimeraX include lights? Kristen: I just checked, and no, these gltf files do not include lights or camera. Darrell: we might also look at providing U3D which can be embedded in PDFs. Greg: it hasn't been used much. Darrell: probably because it is rather difficult to generate. |
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