Changes between Version 113 and Version 114 of NTTData

Timestamp:

Apr 14, 2022, 1:50:00 PM (4 years ago)

Author:

Elaine Meng

Comment:

--

NTTData

@@ -656 +656 @@
 
 Phil: gave a talk to the structural biology group, showed alphafold PAE plots -- people were very interested and liked the ability to switch between domain and confidence (pLDDT) colorings. Elaine: there's a Youtube video of TomG's recent SBGrid workshop on that topic.
+
+TomG: maybe we can also color by conservation calculated from the giant sequence alignment alphafold uses to covariance.
+
+Phil: people had several suggestions:
+(1) to predict every chain in an existing PDB. TomG: you can do that now, just open that structure first and use "alphafold match" ... however, what you get may have a different albeit similar sequence (top BLAT hit) 
+(2) another request was to draw chain boundaries on the PAE plot for the multichain case.
+(3) for selected residue, color others by their PAE with the selected residue.  Could also color-code pseudobonds, or only draw pseudobonds for certain range of PAE values.
+(4) report X,Y cursor location when over the plot (e.g. residue numbers, chain IDs) TomG: what about on the structure? select the 2 residues? draw a pseudobond between them?
+(5) allow zooming in to regions within the plot
+
+Phil: does predicting in ChimeraX work with a user's Colab Pro or Pro+ plan? TomG: yes, since you sign in to Google it knows you have an account.