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

Steve Chou stevezchou at gmail.com
Thu Feb 14 21:49:44 PST 2019

Hi Elaine,
Thanks for your detailed explanation!
What's the format of the pseudobond file? Should it look like this?
#1/A:13 at NE2    #1/A:502 at MG
All the best,

On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Steve,
> Actually I’m surprised the Mg and water were included (even if present at
> both ends) because I thought they had to be tethered by a bond or
> pseudobond (like a distance measurement) to the biopolymer chain, as
> described here under “Atoms in Common”:
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
> For the case where composition changes, you could add in a fake Mg ion and
> water to the structure that’s missing them, but you’d have to decide where
> to put them.  Also it was my understanding that they had to be tethered to
> the biopolymer chain (e.g. add distance measurement, which can then be
> hidden), but maybe that requirement has changed, or the Mg does already
> have a metal-coordination pseudobond to the biopolymer.
> Or if you don’t care if the Mg or water move during the morph, you could
> just display those atoms from the original model (that was input to
> morphing) even though they are not present in the trajectory.
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou at gmail.com> wrote:
> >
> > Thanks, Elaine!
> > You command "rainbow structures" works beautifully.
> > There is "a Mg ion" and "a water molecule" in the two conformations.
> > (1) If the two conformations have exactly the same compositions (by
> shifting the structure), the  "Mg ion" and the "water molecule" do not
> follow the same path as the protein.  They move but separate from the
> protein.
> > (2) If the two conformations have slightly different compositions, the
> "Mg ion" and the "water molecule" do not show up in the morphed pdb
> ensemble.
> > Is there a way to morph the specific components properly?
> > Steve
> >
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