Hi Reza, In general, not necessarily related to Chai-1 or any prediction methods, you can show the sequence of a protein in the Sequence Viewer, and selections in one (sequence or 3D structure) are reflected in the other. Show chain sequence with menu: Tools... Sequence... Show Sequence Viewer, or you can open sequences from UniProt, or sequence alignment files, etc. that will associate with your structure if the sequence is similar enough. See Sequence Viewer help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> Also in general, you can superimpose protein structures with the Matchmaker tool (in menu under Tools... Structure Analysis) or "matchmaker" command to have it figure out the residue-residue correspondences for you, or "align" command if you want to specify exactly which pairs of atoms to use. See help pages: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> 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 Jan 29, 2025, at 1:21 PM, Reza Salavati, Prof. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom Thank you for getting back to me. It was very helpful. Can the files you open be easily manipulated by selecting amino acids on the sequence or structure? Is there a way to superimpose and compare a protein bound with two different ligands? Best Reza