Hi Rebekah, Step 3 can be done with command "sequence align" specifying the already-open sequence window(s) contents as explained in that page, using the IDs shown in the title bars of those windows: https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align

You might need to then associate the structure with a sequence in the resulting pairwise sequence alignment window, if it's not already associated automatically.

Step 4 can be done by (A) showing the conservation header in the pairwise alignment window. If not shown automatically, you can use the sequence window context menu Headers section to show it. https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context

(changing how it is calculated if you like using the context menu Settings, the Headers section). Conservation values may be more meaningful if you had more than two sequences in the alignment, however, but I understand if you are simply trying to highlight all the differences with one other sequence. https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings

...then using command "color byattr" with attribute "seq_conservation" as in the tutorial on coloring by conservation: https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html

Example using commands only (most steps could be done with menus/GUIs instead but would take even more typing to explain):

open 2gbp seq chain /A open uniprot:araf_ecoli seq align 1/A:1,araf_ecoli:1 color byattr seq_conservation palette cyanmaroon novalue yellow

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 16, 2024, at 1:03 PM, Rebekah Dyer via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hello,

I’m wondering if there’s a way to do the following with ChimeraX:

• Open structure with associated sequence (seqA) • Open a separate sequence file (seqB) with no associated structure • Align seqB to seqA • Color residues on structure of seqA protein by conservation between seqA and B

I’ve managed to complete steps 1 and 2, but am stuck on step 3. Any help or advice would be greatly appreciated!

Best,

Rebekah Dyer, Ph.D. (she/her) Staff Enzyme Scientist | Dexcom 6350 Sequence Dr. | San Diego, CA, 92121