Refreshing ChimeraX - ChimeraX slows down after surface generation
Hi I am currently using the ChimeraX Daily version - UCSF ChimeraX version: 1.2.dev202102050202 (2021-02-05). I am working with the pdb: 6j5k - a slightly large protein. If I 'hide atoms' and only 'show cartoons', I can navigate the protein visualisation using my mouse quite well - rotations, translations, zooming etc. However, once I generate the surface and then adjust the slider-side-view to adjust the views to visualise certain aspects of the protein, I have noticed that the computer becomes exceedingly slow to render even small rotations using the mouse - I can understand that this might be because the protein is big. However, the next part - if the surfaces were now deleted and only cartoons are shown in the same session (as in the beginning), the computer is exceedingly slow for mouse work - rotations, translations, slider-view etc. Is there some way to refresh and regain back this agility and remove this hysteresis? The only workaround seems to be to close ChimeraX and then reopen it again, but this is not slightly more tedious if we have to close and reopen every time I make a surface. The commands I have used are: open 6j5k; hide atoms; show cartoons surface #1 enclose #1 Then try to navigate... ~surface; show cartoons And then navigating again.... If there could be some work-around, or a new fix in the ChimeraX_version, it would be really helpful for working with large proteins seamlessly. Thanks Yaikhomba
Hi Yaikhomba, (1) ~surf only hides the surface. You can see it's still there using the disclosure triangle for the main model in the Model Panel, to show its submodels. To get rid of the surface, close it from the Model Panel, or use command "surface close" (2) another thing is to switch simple lighting, since the ambient shadows calculation in fancier lighting may slow things down a little. E.g. "light simple" command or click the toolbar icon that looks like a spotlight. 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 13, 2021, at 3:52 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I am currently using the ChimeraX Daily version - UCSF ChimeraX version: 1.2.dev202102050202 (2021-02-05).
I am working with the pdb: 6j5k - a slightly large protein. If I 'hide atoms' and only 'show cartoons', I can navigate the protein visualisation using my mouse quite well - rotations, translations, zooming etc.
However, once I generate the surface and then adjust the slider-side-view to adjust the views to visualise certain aspects of the protein, I have noticed that the computer becomes exceedingly slow to render even small rotations using the mouse - I can understand that this might be because the protein is big.
However, the next part - if the surfaces were now deleted and only cartoons are shown in the same session (as in the beginning), the computer is exceedingly slow for mouse work - rotations, translations, slider-view etc.
Is there some way to refresh and regain back this agility and remove this hysteresis? The only workaround seems to be to close ChimeraX and then reopen it again, but this is not slightly more tedious if we have to close and reopen every time I make a surface.
The commands I have used are: open 6j5k; hide atoms; show cartoons surface #1 enclose #1
Then try to navigate...
~surface; show cartoons
And then navigating again....
If there could be some work-around, or a new fix in the ChimeraX_version, it would be really helpful for working with large proteins seamlessly. Thanks Yaikhomba
The slowness is from computing the clip caps of the surface. When you use clip planes in side view and the intersect the surface the hole in the surface is covered with a flat surface — computing that is what is slow. You can turn clip caps off with command surface cap off Tom
On Feb 13, 2021, at 9:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yaikhomba, (1) ~surf only hides the surface. You can see it's still there using the disclosure triangle for the main model in the Model Panel, to show its submodels. To get rid of the surface, close it from the Model Panel, or use command "surface close"
(2) another thing is to switch simple lighting, since the ambient shadows calculation in fancier lighting may slow things down a little. E.g. "light simple" command or click the toolbar icon that looks like a spotlight.
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 13, 2021, at 3:52 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I am currently using the ChimeraX Daily version - UCSF ChimeraX version: 1.2.dev202102050202 (2021-02-05).
I am working with the pdb: 6j5k - a slightly large protein. If I 'hide atoms' and only 'show cartoons', I can navigate the protein visualisation using my mouse quite well - rotations, translations, zooming etc.
However, once I generate the surface and then adjust the slider-side-view to adjust the views to visualise certain aspects of the protein, I have noticed that the computer becomes exceedingly slow to render even small rotations using the mouse - I can understand that this might be because the protein is big.
However, the next part - if the surfaces were now deleted and only cartoons are shown in the same session (as in the beginning), the computer is exceedingly slow for mouse work - rotations, translations, slider-view etc.
Is there some way to refresh and regain back this agility and remove this hysteresis? The only workaround seems to be to close ChimeraX and then reopen it again, but this is not slightly more tedious if we have to close and reopen every time I make a surface.
The commands I have used are: open 6j5k; hide atoms; show cartoons surface #1 enclose #1
Then try to navigate...
~surface; show cartoons
And then navigating again....
If there could be some work-around, or a new fix in the ChimeraX_version, it would be really helpful for working with large proteins seamlessly. Thanks Yaikhomba
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participants (3)
-
Elaine Meng -
Tom Goddard -
Y. Mutum