Changes between Version 94 and Version 95 of NTTData

Timestamp:

Feb 17, 2022, 2:31:09 PM (4 years ago)

Author:

Elaine Meng

Comment:

--

NTTData

@@ -552 +552 @@
 TomG: spending much of my time on !AlphaFold and that is highly relevant to cryoEM. Is there a way we can put this in the SOW within the cryoEM section? R01 renewal application does include this area (and the MM/MD stuff below), but its funding would not start until 2023, leaving a year gap. Darrell: if you think it is important for cryoEM we would trust you on that. TomG: how about interactive MD with cryoEM fitting? Darrell: can you give more details... TomG: all atom, OpenMM, AMBER-type force field, ... parametrization of nonstandard residues requires a lot of work. Chimera has minimization, ChimeraX not yet. Phil: dock prep & minimization within a year would be useful (as opposed to having to wait a year for our R01 renewal to kick in).
 
+Meghan: (in agreement with what Darrell said earlier) don't overthink it, since we would generally be OK with your proposing items that fit the needs the larger user community.
+
+Darrell: we couldn't use Modeller but maybe !ModBase fetch would be another useful addition. Darrell: the strength is in features working together (say !AlphaFold + fitting, etc.), just don't want to make you extend the program in ways that don't fit your brand, per se.  Does MD fit your brand? TomG: sounds like our reviewers :-) ... we adjusted our R01 accordingly.  Darrell: we all agree integration is key, (Chimera(X) as "platform") as well as interactivity. Both of these terms can be used in the SOW.  Darrell: what we are trying to build for the cryoEM folks is analogous to NIH3D.  Take in a dataset and create outputs useful for different purposes (publication images etc.). Maybe cryoEM tools Philip has employed in that pipeline could be useful within ChimeraX. Philip: we use IMOD, need to figure out how to run it in a headless environment.
+
+Phil: manual interactive segmentation in VR would be a game-changer. If you could go inside the model and adjust the surface or the fill of a 3D region it would be very useful.