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