Show atom style as spheres and stick simultaneously
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
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@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
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@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@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
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@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@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@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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you for the clarification, Elaine. Mary
On Thu, Feb 10, 2022 at 8:42 AM Elaine Meng meng@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@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@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@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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
-
Elaine Meng -
Mary Liu