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

[Elaine Meng]

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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