[chimerax-users] Can ChimeraX morph between two surfaces?

[Steve Chou]

Dear Elaine,
Thanks for your fast reply.
I (1) saved the trajectory as a multi-model PDB file (11 models, like an
NMR ensemble),
(2) loaded the ensemble PDB back to ChimeraX,
(3) rendered each model as a surface,
then (4) tried to color the surfaces as a rainbow, but the last step [step:
(4)] only produces red surfaces, not a rainbow.
*rainbow chain palette red:blue*
*rainbow polymers palette red:blue*
Steve

On Thu, Feb 14, 2019 at 12:25 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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 at 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
>
>

-- 
Steve Chou
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20190214/7d0a9c40/attachment.html>