Changes between Version 1 and Version 2 of 2023-6-22

Timestamp:

Jun 22, 2023, 12:16:14 PM (2 years ago)

Author:

Tom Goddard

Comment:

--

2023-6-22

@@ -14 +14 @@
 = Discussion Notes =
 
+* Download maps for Chimera
+  - Greg will investigate porting Chimera usage world maps to ChimeraX (download, registration, web service, toolshed).
+  - Download, registration, web service world maps were auto-generated for Chimera, broken by plato update to python 3.
+  - Uses geoIP PyPi package and javascript.
+
+* Sendmail problems
+  - Sendmail problems sending cgl email after plato update.
+  - Scooter thinks sendmail starts before beegfs mounted and so can't access new certificates on beegfs.
+  - Restarting sendmail seems to have fixed it.
+  - Plan is to move certificates off beegfs to local disk.
+
+* Plato operating system update
+  - Crick has been updated to Rocky 8, not all services tested.
+  - Toolshed, SPOKE build, SFLD working on crick.
+  - plato-backup still needs to be updated to Rocky 8.
+  - Redhat announced yesterday plan to restrict source code access which may effect Rocky, Alma and other Linux distros.
+
+* ChimeraX paper in Protein Science
+  - Made outline focussed on model building tools.
+  - Scooter created google doc, contents copied here.
+
+{{{
+Deadline: July 31
+ISOLDE Paper in the same issue
+Have a cross-over
+
+E.g. Atom typing
+
+Main themes: 
+  Model Building
+  Important third party bundles/extensibility
+
+Key features to discuss:
+  Alphafold/ESMFold
+  Phenix
+  ISOLDE
+
+Standard workflow for unknown structure:
+  Cryo-EM
+  Alphafold/modeller
+  ChimeraX fitting
+  Phenix
+  ISOLDE
+
+Bundles:
+  SEQROW
+  XMAS
+  StarMap
+  ARTIAX
+  StrudelScore/QScore
+  ISOLDE
+
+ChimeraX Tools:
+  De novo building
+    AddH
+    Pubchem fetch
+    Smiles fetch
+    IUPAC fetch
+    Peptides and nucleotides
+  Rotamers
+  Alphafold
+  Phenix bundle
+  ESMfold
+  Modeller
+    Comparative
+    loops
+  AddCharge
+  DockPrep
+  VR/Standalone VR
+}}}
+
 = Action Items =