One more point is that matchmaker was intended even for fairly low sequence similarity. You can downweight the amino acid type part of the score relative to secondary structure, or even omit it entirely (secondary structure score weighting 1.0 instead of 0.3), and/or use a longer-evolutionary-distance residue type matrix. Just another thing to try if you have only tried matchmaker with the default parameters. Whether this works depends on how good a signal there is in alignment of secondary structure elements. Elaine
On Oct 3, 2025, at 2:27 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Semi related - a trick we have used for alignment in cases where the fold is conserved but doesn’t align well with matchmaker is to use molmap to make a map from the target model (perhaps at 12 A to start), then use fitmap to fit the search model to that. Molmap at higher resolution can then be used for more precise alignment. This often works where matchmaker fails.
Cheers Oli
On Oct 3, 2025, at 5:06 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Sorry, I forgot you mentioned that matchmaker doesn't work (sequences too dissimilar) -- in that case, you could try fitting the backbone atoms of specified residues in the two structures with "match" instead. Since "match" doesn't figure out the alignment for you, you'd have to explicitly give the residue ranges, and since the residue types are different, use only the backbone atoms or some subset of the backbone atoms such as alpha-carbons. Example:
match #2:10-88@n,ca,c,o #1:5-83@n,ca,c,o
Elaine
On Oct 3, 2025, at 1:54 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I guess another possibility is to superimpose the model onto 1fha (such as with the Matchmaker tool or command) in hopes that they superimpose well enough for the same center to work, but I don't know how successful that would be.
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