Dear ChimeraX team,
I have been working with analyzing AlphaFold-predicted structures in ChimeraX and have a few queries/suggestions.
1. Color palette for PAE Maps: One of the outputs from ColabFold is a PAE map rendered in a blue-white-red color palette. I find this color scheme very useful, and the command "alphafold pae #1 palette bluered" is working well for changing the color gradient into blue-white-red in PAE map. I was wondering if it could be integrated as a clickable option in the PAE map settings in ChimeraX, similar to the existing "Color plot rainbow" or "Color plot from structure" options.
2. Alphafold contacts color palette: I'm also interested in changing the color palette for alphafold contacts to match the bluered color scheme. While I attempted to change the color palette using the command "alphafold contact #1 /A to /B distance 5 palette bluered", it resulted in all contacts being colored red, without the expected color gradient. I'm curious if there's an alternative approach or if this could be an added feature in future updates.
3. Residue selection and visualization based on PAE cut-off: Lastly, I'm looking for a method to selectively visualize the connections between certain residues based on a PAE cut-off. For example, using the command "alphafold contacts /A to /B distance 5", I can visualize all the residue connections between A and B under a distance of 5. However, this also displays connections that are poorly predicted (i.e., yellow or red lines corresponding to PAE >15). I'd appreciate if you could suggest a way to filter these poorly predicted connections or provide an option for this in the software.
Thank you in advance!
Best regards, Ah-Ram