Changes between Version 5 and Version 6 of NIAID2023

Timestamp:

Jun 8, 2023, 1:58:41 PM (2 years ago)

Author:

Elaine Meng

Comment:

--

NIAID2023

@@ -40 +40 @@
 7. Administration 
  a. Submit monthly written reports of accomplishments
+
+== 6/8/2023 ==
+
+Phil, Kristen Browne, Meghan, Bhinnata(?); Zach, TomG, Eric, Elaine, Greg 
+
+Phil will be away on vacation (Europe) next time
+
+3D pipeline issues:  
+- Kristen had one rendering that came up blank, Phil did not test that case yet
+
+- Kristen: did we want to increase quality on small molecules too? Phil did not get to that yet
+
+- Kristen: EMDB 10067 was not using recommended contour level. Phil was going to investigate that one further and if needed, make a ticket for it. 
+
+- Phil: there were some updates for the disconnected pseudobond issue. Eric: submitted new version of NIH3D bundle with preset that makes missing segment pseudobonds go between CA atoms. 
+
+- Phil: regarding quality of surface models, did some test prints of 4 molecules of different sizes, 3DPX (old Chimera) vs. NIH3D (new ChimeraX). Still need to investigate changing grid size and sharpBoundaries parameter. Old ones from Chimera are smoother.  Tom: We need to know exactly which commands/options were used to make the 3DPX surfaces.  Phil: we were using the "grid" option for more robust surfaces in Chimera. TomG: in that case, ChimeraX should be able to generate the same surfaces if we give it the right option values, since it's the same algorithm.  Another important factor is whether hydrogens were added. TomG: sharpBoundaries significantly increases the number of vertices.  Megan sent pictures for 6eee, and TomG and Elaine both compared Chimera and ChimeraX grid surfaces, spacing 2.179, and both looked bad/chunky.  Phil: I will send data files, commands that were used, etc.  How to send? email?  Eric: how did you count vertices?  Phil: I load the files into Blender. I used to do it in Meshlab.
 
 == 5/25/2023 ==