Multi-sampling in ChimeraX
Hi all,
May I ask is there a super-sampling option in ChimeraX to turn on so that the edges of maps are smoother?
Somethiing equivalent to Tools - Viewing Controls - Effects, there is a Graphics quality, you can choose subdivision and whether to turn on multisample.
Thanks!
Best, Zhen
Hi Zhen, I could not find any mention of multisampling in the ChimeraX documentation -- maybe the other developers can say whether this is still relevant on current machines with higher-resolution displays.
There is a "graphics quality" command but it is for atomic and ribbon representations. https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality
Map triangulation can be adjusted with "volume" command options, see subdivideSurface, etc.: https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf
For molecular surface see the "gridSpacing" option of "surface" https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html
There is also something called "supersampling" but it only relates to the process of saving images, not the interactive appearance. https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 13, 2022, at 11:13 PM, Chen, Zhen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
This Message Is From an External Sender This message came from outside your organization. Hi all,
May I ask is there a super-sampling option in ChimeraX to turn on so that the edges of maps are smoother?
Somethiing equivalent to Tools - Viewing Controls - Effects, there is a Graphics quality, you can choose subdivision and whether to turn on multisample.
Thanks!
Best, Zhen
Hi Zhen,
There is currently no multisampling option in ChimeraX. As Elaine mentions you can use the supersample option when saving an image (e.g. "save mymol.png super 3"). To get sharper appearance of graphics and user interface on the screen a nice approach is to use a 4K display.
When looking at maps use "step 1" in the Volume Viewer panel to show full resolution. If it is "step 2" (when you open a large map it may start at step 2) it will use only every other grid point along each axis and the surface will be more jagged.
And if you want to make your map appear smoother in the graphics you can resample it on a finer grid. For example EMDB 12654 has a grid spacing of 1.5 Angstroms. To resample it at 0.8 Angstroms.
open 12654 from emdb volume resample #1 spacing 0.8
The appearance is then somewhat smoother as shown in the attached images.
Tom
EMDB 12654 at original 1.5A grid spacing.
EMDB 12654 resampled at finer 0.8A grid spacing.
On Sep 13, 2022, at 11:13 PM, Chen, Zhen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
This Message Is From an External Sender This message came from outside your organization. Hi all,
May I ask is there a super-sampling option in ChimeraX to turn on so that the edges of maps are smoother?
Somethiing equivalent to Tools - Viewing Controls - Effects, there is a Graphics quality, you can choose subdivision and whether to turn on multisample.
Thanks!
Best, Zhen _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom and Elaine,
Thanks a lot for your quick response.
Yes the supersample option when saving an image solves my problem (for manuscript preparation)!
Best, Zhen ________________________________ From: Tom Goddard goddard@sonic.net Sent: Wednesday, September 14, 2022 9:34 AM To: Chen, Zhen Zhen.Chen@ucsf.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Multi-sampling in ChimeraX
Hi Zhen, There is currently no multisampling option in ChimeraX. As Elaine mentions you can use the supersample option when saving an image (e. g. "save mymol. png super 3"). To get sharper appearance of graphics and user interface on the screen ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization.
ZjQcmQRYFpfptBannerEnd Hi Zhen,
There is currently no multisampling option in ChimeraX. As Elaine mentions you can use the supersample option when saving an image (e.g. "save mymol.png super 3"). To get sharper appearance of graphics and user interface on the screen a nice approach is to use a 4K display.
When looking at maps use "step 1" in the Volume Viewer panel to show full resolution. If it is "step 2" (when you open a large map it may start at step 2) it will use only every other grid point along each axis and the surface will be more jagged.
And if you want to make your map appear smoother in the graphics you can resample it on a finer grid. For example EMDB 12654 has a grid spacing of 1.5 Angstroms. To resample it at 0.8 Angstroms.
open 12654 from emdb volume resample #1 spacing 0.8
The appearance is then somewhat smoother as shown in the attached images.
Tom
EMDB 12654 at original 1.5A grid spacing. [cid:C239FF81-040B-41CC-B197-20E23E99E8D1]
EMDB 12654 resampled at finer 0.8A grid spacing. [cid:9B9A9E26-4502-4971-8ACA-7D8015254680] On Sep 13, 2022, at 11:13 PM, Chen, Zhen via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
This Message Is From an External Sender This message came from outside your organization. Hi all,
May I ask is there a super-sampling option in ChimeraX to turn on so that the edges of maps are smoother?
Somethiing equivalent to Tools - Viewing Controls - Effects, there is a Graphics quality, you can choose subdivision and whether to turn on multisample.
Thanks!
Best, Zhen _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Chen, Zhen -
Elaine Meng -
Tom Goddard