Hi Emir, I'm not sure what causes that black middle section of your sequence plot, probably something odd about your sequence -- maybe it is all Xs in the middle? If you hover the mouse over the plot it reports the query residue you are over and that may help you find which residues correspond to the middle black region. Also you could open one of the Foldseek hits then use the command sim seqalign #2 To show the sequence alignment Foldseek gave between the query and that hit (model #2). Tom

On Mar 11, 2025, at 12:13 PM, Emir MALOVIC <malovic@wisc.edu> wrote:

Hi Tom,

Here is PNG export of the sequence plot.

Oh, I see, okay.

Yeah, that would be useful to add if possible, and for any table of that matter!

Thank you! Emir

From: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> Sent: Tuesday, March 11, 2025 2:06 PM To: Emir MALOVIC <malovic@wisc.edu <mailto:malovic@wisc.edu>> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] General ?s - Foldseek (Sequence Plot) and Similar Structures Table

Hi Emir,

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.

Tom

<foldseek_seqs.png>

...

On Mar 11, 2025, at 9:04 AM, Emir MALOVIC via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto: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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...> <sequences.png>