On Nov 16, 2025, at 8:32 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
For coloring by RMSD specifically, I thought it might work to use "perframe" to do the RMSD coloring (as in your first question) at each step of the morphing trajectory. However, I could not get it to work; even though the RMSD histogram on the sequence alignment was changing, the coloring stayed the same through the whole morph.
Got this to work, with help from a colleague. Here is an example: open 2gbp open 2fw0 mm #2 to #1 show true color byattribute seq_rmsd #2 palette bluered range 0,10 morph #1,2 sequence disassociate #2/A perframe "color byattribute seq_rmsd #3 palette bluered range 0,10"; coordset #3 1,51; wait 51; ~perframe ...where the last long set of commands starting with perframe should be all one line... Also, this is just an example; if you were doing this, you might want to use a different coloring palette or a different range of values. Elaine