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

[Elaine Meng]

Hi Steve,
You want “rainbow structures”:

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential>

Best,
Elaine

> On Feb 14, 2019, at 12:21 PM, Steve Chou <stevezchou at gmail.com> wrote:
> 
> 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
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users