Hi Steve, Yes, you have to have equal numbers of chains in the two structures on either end of a morph. This is in the “Limitations" <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations> You cannot morph only the surfaces; instead you would morph the atomic structures and then show surface for the trajectory as it morphs (in effect, you would just see the surface morphing). I can’t think of any easy way to gradually change the color of the surface over the trajectory, though. A somewhat tedious way would be to save the trajectory as a multi-model PDB file, then reopen (it would show all the frames at the same time like an NMR ensemble), then “rainbow” with your desired palette, say red->blue, then surface each one, then show each one in trajectory order, hiding the others. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 14, 2019, at 9:13 AM, Steve Chou <stevezchou@gmail.com> wrote:
Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou