Hi Tyler, The change in opacity can be very rapid from 0.99 to 1.0 in volume image display style. To understand what is going on it is useful to look at the volume command transparency option documentation • <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#top> transparency value <> Transparency values range from 0.0 (fully opaque) to 1.0 (fully transparent). For image displays, this setting gives the slab thickness (as a fraction of the dataset's shortest dimension, range 0.0–1.0, default 0.5) that gives the transparency indicated by threshold height on the histogram (details... <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#soliddetails>). By default, more transparent voxels are made dimmer (see dimTransparentVoxels <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#dimvox>). The behavior you see where your orange is not very visible at threshold height 0.99 and then is very visible at 1.0 is because the orange region is quite thin compared to the thickness of the volume box, and the those heights control transparency for a thickness of 0.5 times the volume box size. In otherwords you would get opacity 0.99 (which would be very visible) if the orange region had a thickness of 0.5 of the box size. But since it likely has image thickness of 1/20 of the box size it is not very opaque. At any rate, you can probably improve the situation by changing the volume transparency setting from its default 0.5 using volume #1 style image transparency 0.05 This will also change the height values you need for the other colors. I'm not sure if this will help you since I don't have your data to try it. It gets tricky to control the transparency to show both thin and thick regions at the same time without having the thick hide the thin. You can also try heights 0.99, 0.991, 0.992, 0.993, ..., 1.0 to get a gradual transition. Tom
On Mar 5, 2024, at 1:03 PM, Tyler Luchko (Lists) via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello,
I’m trying to fine tune the intensity of my volume image, but there is a large discontinuity between an intensity of 0.99 and 1 that is causing me problems. Using the following script, I get
volume #1 style image volume #1 colormapongpu true volume #1 level 0,1 color black level 1,.55 color white level 2,.6 color blue level 4,0.99 color orange
<orange-99.png>
Changing the last list to
volume #1 level 0,1 color black level 1,.55 color white level 2,.6 color blue level 4,1 color orange
I get
<orange-1.png>
The last level goes from barely visible to completely opaque. I don’t know if this is the intended behavior or not, but I would like to have a smooth transition to full intensity. Is this possible?
I notice that for levels between 0 and 1, the intensity seems to work as I expected. It is only for levels greater than 1 that I notice this behavior.
I am on a Mac using version 1.7.1. The MRC file is 59 MB, so I have not included it.
If it helps, the visualization is trying to show the water density around methanol (not shown) relative to bulk. Black (0) is zero density, white (1) is bulk density, blue (2) is 2 times bulk density, and orange (4) is 4 time bulk density.
Thank you,
Tyler_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/