Changes between Version 6 and Version 7 of NIAID2024

Timestamp:

Apr 11, 2024, 2:01:41 PM (19 months ago)

Author:

Elaine Meng

Comment:

--

NIAID2024

@@ -85 +85 @@
 == 4/11/24 == 
 
+TomG, Eric, Zach, Greg, Elaine, Scooter; Phil, Kristen, Meghan, Mike Bopf, Bhinnata
+
+Zach: did you see the email I sent about a radiology conference later this year, are you going?  Meghan: someone will go but we may not be hosting a booth. May be useful for you to attend just to learn, keep it in mind.
+
+Scooter: we still don't have a contract finalized even though we were told it was fine to start the work. I'll email and ask for status.
+
+Meghan: what's going on with workflows? Kristen: we need to figure out what we want re AlphaFold, still haven't gotten a list of specific requests.  Quick submit is when the user enters an accession code (will be obtained using ChimeraX fetch) rather than uploading their own structure.
+
+Scooter: we should talk about AlphaFold and GLTF. We would like to add a "publish to Schol-AR" feature in ChimeraX using REST interface. Developer Tyler Ard is a medical imaging guy and has given us some feedback about the ChimeraX tools.  We would like to visit him at USC, give demos, discuss features, and try to engage his colleagues as well.
+
+TomG: Meghan's powerpoint gltf example used an older ChimeraX. Newer ChimeraX (Oct 2023) gltf export has better treatment of color, so looks better in powerpoint. Discussion of whether the vrmls will then need correction since those converted from the older gltfs are fine.  Meghan: let's test with newer ChimeraX. Phil: it looks good enough with newer ChimeraX that we don't need any special preset for gltf export for powerpoint.
+
+Kristen: another possibility is color STL. Greg: recommend staying away from STL. Kristen, Meghan: or 3MF or USC (universal scene description).  Kristen: there are various flavors, USC-Z etc.
+
+TomG: should NIH3D put in lighting, or leave that to the end user's application?  Kristen: probably better to leave it out so that you don't get stuck with both lighting from the exported file and the application, and no reasonable way to remove lights.
+
+Discussion of lighting direction vs. camera direction.  If there is a headlight you avoid dark sides of models, but that approach can overly wash out white or other light-colored models.  
+
+Phil: for AlphaFold, we probably want at least 2 colorings, by PAE domain and by pLDDT. Tom: pLDDT is well-known but PAE domain coloring is more specific to ChimeraX and may require more explanation or at least thought as to whether you really want to make it available.  Parts of more than one chain can be assigned to the same PAE domain. Phil: for quick submit, it will be only one protein. My instinct is that we still want to include it for alphafold database entries, along with a good explanation.  Phil: other issue is whether to hide low-pLDDT spaghetti.  What is a reasonable cutoff? Tom: pLDDT 50. Tom: keep in mind that PAE values are in a separate file than the structure. ChimeraX alphafold fetch gets both files.
+
+Current thinking is we need more presets: both with and without spaghetti, 2 alphafold coloring schemes, and all the existing color schemes of both ribbons and surfaces.  Elaine: do you really need a combinatorially expanded set of presets, when some of these differences would just be a single command? Eric: how about a modifier preset? Then still simple but less duplicative.  To get a specific view, you'd use preset A followed by modifier preset B.
+
+Phil: do you need any more specifics? Eric: do you need missing-structure pseudobonds where the spaghetti is hidden or excised?  What about surfaces? Will think about the implementation details.  Tom: I have various doubts (a) that getting rid of the low pLDDT, can remove parts of helices, even buried cores, etc. and give weird results. (b) also, pLDDT coloring is useful for ribbons, probably not surfaces, have not seen it used for surfaces. Others: would simplify the preset situation to omit some of these options.
+
 == 3/28/24 ==