Hi Sam, The undocumented 'ks' (keyboard shortcut) command can select residues between two selected residues. Namely, "ks ri" (mnemonic: keyboard shortcut residue interval) will do it. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 21, 2026, at 8:44 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Samuel, Well, "selection" can mean a couple of different things. If you mean selected in the structure, which is shown in green boxes on the sequence alignment:
(1) if you have two separate residues selected, you would see two green boxes on the alignment. You can then drag a box around the residues in that sequence in the alignment window, starting with the first one and ending with the last one (in English this could also be called "selection" but on the alignment and not necessarily in a structure unless a structure is associated with that sequence). However, as soon as you start to draw the box it will erase the existing structure selection and simultaneously create a new one, so you have to first make sure you remember where in the sequence window are the starting and ending residues. Or if you didn't have anything selected to start with, you can just drag a box that covers the stretch of interest. The colored box that you just dragged with dashed outline is the "active region" and in the Sequence Viewer context menu, choose Edit... Copy Sequence... This will bring up a dialog with a choice to restrict the copy to the active region. The copy is to the clipboard, and can be pasted in the usual ways, text editor window or whatever.
(2) Or, you could have started by selecting the whole stretch of residues in the structure which will show as a continuous green box on the sequence. Either way, if that region (colored box on alignment) has a dashed outline it is already the active region and you can proceed as above without dragging a new box.
A context menu is shown by right-click on the tool (or for Mac trackpad or single-button mouse, Ctrl-click replaces “right-click” for showing context menus). See Sequence Viewer, regions, context menu. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#regions> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context>
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 Apr 21, 2026, at 2:21 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Not sure if I'm missing this but there are a few sequence selection and export tools that I can't seem to find an easy way to do:
• Is there a way to select two locations on a protein chain and then expand the selection to include all the residues between those two points? • If a continuous stretch of residues is selected, is there a way to print the sequence to the log or to copy it to the clipboard? • In the sequence view, is there a way to select a stretch of residues and then copy that to the clipboard? In general it would be really nice if copy worked in the sequence view window on selected residues
I'm aware that I could script this functionality but it does seem to the sort of thing that might be possible in the vanilla installation. KR, Sam
Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma
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