Changes between Version 1 and Version 2 of Dev2024-2-5

Timestamp:

Feb 5, 2024, 4:05:45 PM (21 months ago)

Author:

Tom Goddard

Comment:

--

Dev2024-2-5

@@ -1 +1 @@
 = ChimeraX Developer Meeting =
 
-Attendance: Greg, Zach, Tom, Eric
+Attendance: Zach, Tom, Eric
 
 February 5, 2024
@@ -20 +20 @@
 = Discussion =
 
+* Windows Chimera build charge calculation
+  - Eric fixed copying of fortran library to distribution.
+  - Charge calculation on 2gbp worked.
+
+* Chimera on Nvidia 4070
+  - On vive.cgl.ucsf.edu Windows 10 showing only black graphics pane.
+  - Replaced Quadro P6000 with Nvidia 4070 a couple weeks ago (for VR NIAID testing).
+  - Chimera problem was it was using stereo mode.
+  - Fixed by switching to mono camera.
+
+* Speech to text for ChimeraX control
+  - Scooter asked Zach if we can demo speech to ChimeraX commands during NIAID visit.
+  - Zach trying OpenAI Whisper and a Google speech to text service.
+  - Zach says you have to yell to get reliable speech to text.
+
+* AlphaFold group meeting for John Gross lab
+  - Tom giving presentation on running alphafold to find protein-protein interactions tomorrow.
+  - [https://www.rbvi.ucsf.edu/chimerax/data/afbatch-jan2024/rim_dimers.html Slides]
+  
+* SPICE idatm typing
+  - Eric talked to Peter Eastman about extremely unlikely protonation states in SPICE database.
+  - Peter says as long as they are physically possible they are not considered a problem.
+  - Eric will simply drop SPICE entries that cannot be idatm typed.
+  - Will keep ones with exotic protonation.
+  - Goal is to provide these idatm types to train a ML network to predict charges.
+
+* Grafana
+  - Zach says Scooter suggests running it as nightly cron job.
+  - Last try to setup realtime monitoring generated lots of processes that Scooter had to kill, and Zach says all data files were erased.
+
+* mmseqs2 sequence alignment on plato
+  - Tom will try installing mmseqs2 sequence alignment for ColabFold on a plato node.
+  - May use new SSD drive for databases.
+  - Testing to see if ColabFold server will work with Rocky 8.
+  - If it works we may get 1 Tb memory to run a ColabFold sequence server.
+
 
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