[chimerax-users] Show atom style as spheres and stick simultaneously

[Mary Liu]

Thank you for the clarification, Elaine.
Mary

On Thu, Feb 10, 2022 at 8:42 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Mary,
> No, it's the solvent-excluded surface (SES) as shown in this diagram...
> you can see that the SES is the same as the outer VDW surface in some
> areas, but crevices are smoothed out:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
>
> Only the sphere style of atom display is simply VDW spheres.
> Elaine
>
> > On Feb 10, 2022, at 12:11 AM, Mary Liu via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Thank you, Elaine.
> > Is it possible to display the surface dot/mesh with VDW size of only
> side-chain atoms instead of their solvent excluded surface area?
> >
> > Mary
> >
> > On Wed, Feb 9, 2022 at 1:28 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Mary,
> > You cannot show atomic spheres as dots or mesh, although you could make
> them transparent.  To show atoms as both spheres and sticks you would have
> to open two copies of the atoms, however.  Example commands:
> >
> > open 1gcn
> > open 1gcn
> > hide ribbon
> > show atoms
> > style #2 sphere
> > transparency #2 50 target a
> >
> > Alternatively, you could show molecular surface at the same time as the
> stick atoms without opening an extra copy.  You can show molecular surface
> as transparent, or dots, or mesh.  Example commands:
> >
> > open 1gcn
> > hide ribbon
> > show atoms
> > surface style mesh
> > surface style dot
> > surface style solid
> > transparency 50 targ s
> >
> > For details and command options, use help command, e.g. "help style",
> "help surface" or "help transparency"
> >
> > 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 9, 2022, at 4:51 AM, Mary Liu via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> > >
> > > Dear Chimera X users,
> > >
> > > Is it possible to show atom style as spheres and stick simultaneously
> with spheres displayed as dots or mesh so the stick is still visible within
> sphere dots?
> > >
> > > Thank you
> > > Mary
> >
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>
>
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