Hard to know what you are seeing with the ChimeraX Similar Structures sequence plot without an screenshot. The black normally corresponds to aligned residues that are not the same amino acid type as the query. Blue is is for amino acids that are the same as the query, and yellow is highly conserved residues.

As for saving the table of foldseek results, it is automatically saved by ChimeraX as a JSON file in the ~/Downloads/ChimeraX/Foldseek directory, e.g. ~/Downloads/ChimeraX/Foldseek/8p4k_A_foldseek_pdb.sms. Not sure if Excel can turn JSON into a table. Unfortunately it seems that selecting all the table lines and trying to copy and paste is not working on Mac (Command-C copies nothing). I'll ask the ChimeraX table developer Eric if copy and paste could work.

On Mar 11, 2025, at 9:04 AM, Emir MALOVIC via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

Quick question:

When I load the sequence plot, I receive 2 sequence images separated by a very large black space. When I save the image as a PNG, the black space between the sequence images is retained. Basically, the image is mostly black space. Is there a way to change that or is this a bug?

Am I able to somehow copy the Similar Structures table or export it into Excel? A copy/paste function would be ideal and quick.

I am using the Chimera 1.10 dev.

Please let me know at your earliest convenience!
Thank you,
Emir
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