Changes between Version 2 and Version 3 of NIAID2022

Timestamp:

Jul 7, 2022, 1:46:19 PM (3 years ago)

Author:

Elaine Meng

Comment:

--

NIAID2022

@@ -67 +67 @@
 TomG: M1 build should be available sometime next week, pending Riverbank (Phil Thomson?) getting the PyQt commercial wheels working on M1.  We will put it on the download page.
 
-Eric and Elaine: Renumber residues command and GUI are in the daily build, change chain ID command tomorrow, GUI also should be done in a day or two. Phil: very happy to see this, one of the few remaining reasons I go back to Chimera.  Is there a GUI for Color Secondary structure?  Elaine: not currently... we figured the 3 commands were not hard (color helix purple, etc.).  Scooter/Eric will add to list of requests.
-
-Phil: another request is related to the AlphaFold PAE plots.  Default for alphafold fetch is trim true, but then can't get PAE plot.  Must re-fetch with trim false.  Maybe add option to GUI for fetch w/o trim. TomG: another possibility is to make it smarter to work after trimming. Have considered some alternatives, but there are potential pitfalls. Elaine: what about trim false?  TomG: trim true is a better default for alphafold match. Phil: having it work with trimmed structures would be the best.
+Eric and Elaine: Renumber residues command and GUI are in the daily build, change chain ID command tomorrow, GUI also should be done in a day or two. Phil: very happy to see this, one of the few remaining reasons I go back to Chimera.  Is there a GUI for Color Secondary structure?  Elaine: not currently... we figured the 3 commands were not hard (color helix purple, etc.).  Scooter & Eric will add to list of requests.
+
+Phil: another request is related to the !AlphaFold PAE plots.  Default for alphafold fetch is trim true, but then can't get PAE plot.  Must re-fetch with trim false.  Maybe add option to GUI for fetch w/o trim. TomG: another possibility is to make it smarter to work after trimming. Have considered some alternatives, but there are potential pitfalls. Elaine: what about trim false?  TomG: trim true is a better default for alphafold match. Phil: having it work with trimmed structures would be the best.
+
+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.
 
 == 6/9/2022 ==