Changes between Version 3 and Version 4 of NIAID2022

Timestamp:

Jul 7, 2022, 2:01:11 PM (3 years ago)

Author:

Elaine Meng

Comment:

--

NIAID2022

@@ -73 +73 @@
 TomG: have you tried displaying the pseudobonds colored by PAE values (alphafold contacts)? Phil: not yet, but I remember you showed it. Phil: another hangup remembering the right option to get the pkl file (with PAE plot info) monomer predictions.
 
-Phil: having difficulties reading mmCIF headers to get metadata, any pointers? Some types of information can be in multiple different places, depending on the specific file -- not predictable/consistent. TomG: Greg (on vacation) is our main mmCIF guy, but I've written code to obtain specific information like UniProt IDs from those headers. TomG: recommend complaining to RCSB PDB helpdesk when the info (EMDB code or whatever) is missing from what the REST service returns. Scooter: So far, I'm consistently seeing the EMDB codes in _database_2.database_code (and then *sometimes*) in some of the other fields.  Eric: can use graphql to get the information instead of getting the whole header from RCSB PDB.  You can get it for multiple entries at once, returns json. Our tool showing BLAST results uses graphql.
+Phil: having difficulties reading mmCIF headers to get metadata, any pointers? Some types of information can be in multiple different places, depending on the specific file -- not predictable/consistent. TomG: Greg (on vacation) is our main mmCIF guy, but I've written code to obtain specific information like !UniProt IDs from those headers. TomG: recommend complaining to RCSB PDB helpdesk when the info (EMDB code or whatever) is missing from what the REST service returns. Scooter: So far, I'm consistently seeing the EMDB codes in _database_2.database_code (and then *sometimes*) in some of the other fields.  Eric: can use graphql to get the information instead of getting the whole header from RCSB PDB.  You can get it for multiple entries at once, returns json. Our tool showing BLAST results uses graphql.
+
+TomG: have been looking into !ColabFold -- significantly faster and may have other advantages (use of template structures?). Need to ask authors if it's OK for ChimeraX to interface with their server.
 
 == 6/9/2022 ==