Changes between Version 7 and Version 8 of NIAID2023

Timestamp:

Jun 15, 2023, 1:25:33 PM (2 years ago)

Author:

Elaine Meng

Comment:

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NIAID2023

@@ -40 +40 @@
 7. Administration 
  a. Submit monthly written reports of accomplishments
+
+== 6/15/2023 ==
+
+Phil, Kristen Browne, Meghan, Darrell, Bhinnata, Victor Starr Kramer; Zach, TomG, Eric, Elaine, Greg
+
+"Extra" meeting to figure out suitable settings for the desired number of surface triangles (smoothness vs. file size, calculation time, etc.) for NIH3D pipeline.
+
+Phil: established that the requirements for NIH3D and Enduvo are so different that they should just be in separate workflows
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+Phil: turns out the discrepancies between 3DPX (3D print exchange with Chimera) and NIH3D (new pipeline with ChimeraX) were due to different procedure/rules for grid size calculation.  Is this in the scripts or presets?
+
+Eric: presets, but we need to decide on appropriate size limits for switches in resolution, or caps on the number of triangles or vertices.  Calculations for the biggest structures can be extremely slow.  Eric: Tunable parameter is grid size. Another possibility is to go to gaussian surfaces instead of molecular surfaces. TomG: Gaussian surfaces have two adjustable parameters, resolution and grid size. We also noticed that calculation time is not linear in the number of atoms.
+
+Phil: to me, long calculations are OK as along as the user's expectations are managed.  Darrell: I agree, the expectations for a website like NIH3D can be different than for an interactive program like ChimeraX.  Still, we don't want ridiculously huge files that many will not be able to handle. Kristen: in situations where we have to re-run everything, multiday calculations are less feasible.  May also need to warn users specifically that processing will take a long time, and have some kind of indicator to us as pipeline developers that the process is still running/proceeding rather than hung.
+
+Kristen: can we change these parameters?  Elaine: they are command options. Phil: I see the preset-generated commands and then make variations on those commands and try them.
 
 == 6/8/2023 ==