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