Display volume default threshold level
Dear UCSF ChimeraX developers, I am Chenwei Zhang, a PhD student from UBC, Canada. I am currently using ChimeraX for cryoEM density map visualization, which did a really nice job. There's one question I would like to seek answers from you. When I show a density map in ChimeraX GUI, it show automatically show a threshold level. Here's a quick example when I open emd_6272.map file: _Opened emd_6272.map as #1, grid size 108,108,108, pixel 1.02, shown at level 0.0555, step 1, values float32_ May I ask how does ChimeraX get this threshold? Or more generally, how does ChimeraX calculate the density values to get this final threshold value? Is there any command I could use in ChimeraX to extract this value? I tried to find answers in your documentation but failed so I am writing this email for help. Thank you in advance and look forward to your reply. Best, Chenwei
Hi Chenwei, The initial contour level of an isosurface is set to enclose 1% of grid points, except for maps opened by EMDB fetch, which will be shown at the depositor-recommended contour level, if any. For single-plane display, the middle plane along Z is shown initially with a linear ramp in grayscale from the 10th (black) to 99th (white) percentile of values. This is mentioned in the current Volume Viewer help page, but I understand there are a lot of words in our help and it can be hard to find a specific thing! <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> Also, to report the current threshold level you can look in the Volume Viewer dialog "Level" field or use command "volume settings" which will report it in the Log, along with a lot of other settings. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#settings> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 2, 2024, at 1:51 PM, Chenwei Zhang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF ChimeraX developers,
I am Chenwei Zhang, a PhD student from UBC, Canada. I am currently using ChimeraX for cryoEM density map visualization, which did a really nice job. There's one question I would like to seek answers from you. When I show a density map in ChimeraX GUI, it show automatically show a threshold level. Here's a quick example when I open emd_6272.map file: Opened emd_6272.map as #1, grid size 108,108,108, pixel 1.02, shown at level 0.0555, step 1, values float32
May I ask how does ChimeraX get this threshold? Or more generally, how does ChimeraX calculate the density values to get this final threshold value? Is there any command I could use in ChimeraX to extract this value? I tried to find answers in your documentation but failed so I am writing this email for help.
Thank you in advance and look forward to your reply.
Best, Chenwei
Hi Elaine, Thank you so much for your prompt reply and help. It's very useful information. I will carefully read the latest documentation you shared to me and let you know if I still have questions. Have a great weekend! Best, Chenwei On 2024-02-02 14:01, Elaine Meng wrote:
[CAUTION: Non-UBC Email]
Hi Chenwei,
The initial contour level of an isosurface is set to enclose 1% of grid points, except for maps opened by EMDB fetch, which will be shown at the depositor-recommended contour level, if any. For single-plane display, the middle plane along Z is shown initially with a linear ramp in grayscale from the 10th (black) to 99th (white) percentile of values.
This is mentioned in the current Volume Viewer help page, but I understand there are a lot of words in our help and it can be hard to find a specific thing!
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html>
Also, to report the current threshold level you can look in the Volume Viewer dialog "Level" field or use command "volume settings" which will report it in the Log, along with a lot of other settings.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#settings>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 2, 2024, at 1:51 PM, Chenwei Zhang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF ChimeraX developers,
I am Chenwei Zhang, a PhD student from UBC, Canada. I am currently using ChimeraX for cryoEM density map visualization, which did a really nice job. There's one question I would like to seek answers from you. When I show a density map in ChimeraX GUI, it show automatically show a threshold level. Here's a quick example when I open emd_6272.map file: Opened emd_6272.map as #1, grid size 108,108,108, pixel 1.02, shown at level 0.0555, step 1, values float32
May I ask how does ChimeraX get this threshold? Or more generally, how does ChimeraX calculate the density values to get this final threshold value? Is there any command I could use in ChimeraX to extract this value? I tried to find answers in your documentation but failed so I am writing this email for help.
Thank you in advance and look forward to your reply.
Best, Chenwei
-- Best wishes, Chenwei
participants (2)
-
Chenwei Zhang -
Elaine Meng