See the Matchmaker tool (menu: Tools... Structure Comparison... Matchmaker) or "matchmaker" command. Both of these have an option to show the sequence alignment in a window. In the tool, it is in the "Alignment" section and you have to turn on "Show pairwise sequence alignments" <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#top> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#alignment> In the command you would need to include "showAlignment true" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#top> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> Then in the sequence alignment window (Sequence Viewer tool) you can use the context menu to save to a file. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context> ... or another way is to just use the "save" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#sequence> However, that will save the whole sequence alignment, including the parts that are not aligned. In the display of the sequence alignment window there will be orange boxes drawn around the residues used in the 3D alignment, so you could try to manually edit the sequence file yourself using a text-editing program (outside of ChimeraX). However, it may be difficult depending on how much editing is required. That would have both sequences in the file. You can also just show and save the sequence of one protein, e.g. if it is model #1 chain C, command seq chain #1/C <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#chain> ... then save it from the sequence window as above. Again it would be the whole sequence and you would need to manually edit the resulting file, based on the orange boxes in the pairwise sequence alignment. 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 Oct 25, 2024, at 2:34 AM, Mamadou Sangare via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear, I would like to align two protein structures A and B, select and extract the parts of the B sequence that match A in a fasta file.
Thank you for your support.