Changes between Version 5 and Version 6 of Dev2024-1-29

Timestamp:

Jan 29, 2024, 5:19:35 PM (21 months ago)

Author:

Tom Goddard

Comment:

--

Dev2024-1-29

@@ -20 +20 @@
 = Discussion =
 
+* Chimera Windows build
+ - Build is now working after reverting cygwin gcc version.
+ - But sqm is not working in the Windows Chimera because a fortran library was not copied to the build.
+ - Eric added the missing library and will retest on Thursday.
+
+* Networking problem with Elaine's new iMac
+ - Not able to copy the daily build to Elaine's new iMac chopin.
+ - That new machine has no ethernet jack so a dongle is used.
+ - Problem was related to network access control and that there was a switch under the desk.
+ - Removing the switch fixed it.
+
+* RCSB dropping mmtf format
+ - RCSB is dropping the mmtf format which we read.
+ - They recommend using binary mmCIF which we do not read.
+ - Greg may be interested in reading binary mmCIF in the future.
+
+* mmCIF missing atom type field
+ - Greg got bug report of mmCIF failing to read because atom table element type field missing.
+ - That field is mandatory in mmCIF.
+ - Eric says PDB reader has many convoluted rules to guess element type for PDB files that don't have it.
+ - Decided it is not worth supporting mmCIF without element type unless more people complain.
+ - Greg told user that the software writing the file should be fixed.
+
+* Labeling tiled models
+ - Tom wanted labels below 30 tiled alphafold models.
+ - Uses Python script to make 2D labels.
+ - 2D labels are misaligned as soon as you zoom.
+ - 3D labels can only be on atoms, or residues or bonds or pseudobonds, so won't work for maps (e.g. class averages that Oliver Clarke tiles).
+ - One idea is to make label command able to label a model or maybe even just label a fixed scene coordinate.
+
+* Running AlphaFold without Google Colab
+ - Tom looking for ways for users to run AlphaFold besides the limited Google Colab.
+ - Needs Nvidia graphics and Linux.
+ - For UCSF users, Wynton cannot run the 10x faster Colabfold because internet access to sequence server is blocked.
+ - Tom Ferrin and Andrej Sali are seeing if Wynton can unblock some URLs.
+ - Apple is trying to write a backend for XLA (accelerated linear algebra) to use Metal which might allow AlphaFold to run on Macs in the future.  Not working in current version 0.0.5.
+
+* Speech input in ChimeraX for VR
+ - Zach has tried Whisper from OpenAI that runs locally on user's machine, has python library.
+ - Scooter also suggests comparing to a Google speech to text service that also has a python library.
+
+* Selina's medical image tumor segmentation in ChimeraX
+ - Zach showed Selina how to get best rendering of images in ChimeraX.
+ - Zach working on ChimeraX web service backend support to use qsub on Wynton to submit jobs and monitor when the finish.
+
+* Email to Trac
+ - Greg and Eric working to fix trac database.
+ - Eric had to hand resubmit 20 bug reports arriving over the weekend because trac was down.
+ - Greg rebuilt database, also needed to clean up temporary table listing pending ticket number.
+ - Greg says there is a README file in /usr/local/share/Trac on plato describing how to fix Trac.
+ - Requires root to rebuild Trac.
+ - Greg suggested making a script to do it so any of us could sudo to restore database.
+
+* Combine chains
+ - Eric improving combine command to merge two chains with same id into a single chain.
+ - Currently it only is able to make two chains.
+ - Still working with fixing up the merged chain sequence information.
+
+* SPICE database idatm types
+ - Eric working on getting idatm types for SPICE database molecules.
+ - SPICE molecules are in hdf and need custom code to read into ChimeraX.
+ - Main problems now are idatm types that disagree with protonation state of database molecules.
+
+* Email DKIM support
+ - Greg plans on making plato outgoing email sign with DKIM.
+ - This prevents sending plato email from unauthorized servers.
 
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