Changes between Version 6 and Version 7 of NIAID2023

Timestamp:

Jun 8, 2023, 1:59:21 PM (2 years ago)

Author:

Elaine Meng

Comment:

--

NIAID2023

@@ -56 +56 @@
 - 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.
+- 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.  Kristen: different software will give you different counts.
 
 == 5/25/2023 ==