Hi Ah-Ram,

Thanks for the suggestions.

1. I could add a blue to red palette option for the AlphaFold PAE plot in the drop down menu on that plot. Currently it has rainbow and green choices in the menu. But it is necessary to choose what PAE value red and blue correspond to. I've attached two images using blue = 0, red = 30 (since the PAE range goes to about 30) and blue = 0, red = 10. You see the red = 10 one gives better distinctions in the 0-10 range but everything over 10 will be red. The 0-30 one is mostly all blue, so doesn't let you discriminate values. Since the best range really depends on your model and what you are interested in it is hard to choose default palette ranges. That is why we have the command, so you can do it however you want. I made the two images with

alphafold pae #1 palette bluered range 0,10 alphafold pae #1 palette bluered range 0,30

When you don't specify the range option it uses 0,30.

2. When you use the alphafold contacts command palette option it is using the range 0 to 1. That is a bug, and I just fixed it, so now it will use the range 0,30. But that is not a great choice when using the bluered palette and you probably want to specify the range yourself to give a good distinction for pae values in the range 0-10

alphafold contacts :3-6 to :12-15 distance 5 palette bluered range 0,10

3. I agree it would be nice to be able to not show contacts with high PAE values in the alphafold contacts command. So I've added a maxPae option to only show the contacts below a specified pae value. This will be in tomorrow's ChimeraX daily build, dated June 29 or later.

alphafold contacts :3-6 to :12-15 distance 5 maxPae 10

Tom

PAE plot 0=blue, 10=red.

PAE plot 0=blue, 30=red

On Jun 29, 2023, at 1:38

PM, Ah-Ram Kim via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription: