Hi Kelly,

I tried to visualize the tunnel output from caver recently. The workaround is to manually set the atomRadius for each dummy atom of the caver tunnel output. It will be something like this in the script file:

size #2:1 atomRadius 8.45
size #2:2 atomRadius 8.70
size #2:3 atomRadius 9.03
size #2:4 atomRadius 9.45
size #2:5 atomRadius 9.94
size #2:6 atomRadius 10.49
size #2:7 atomRadius 11.10
size #2:8 atomRadius 11.75
size #2:9 atomRadius 11.96
size #2:10 atomRadius 11.78
size #2:11 atomRadius 11.67
size #2:12 atomRadius 11.64
size #2:13 atomRadius 11.69
size #2:14 atomRadius 11.81

Best,

Zheng

On Wed, Apr 19, 2023 at 10:25 AM Kelly May Frain via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I am using ChimeraX to visualise a tunnel found in my membrane protein using caver.
I can put together the protein pdb and tunnel pdb perfectly.
However, crucial to the figure is how the tunnel has a different radius throughout.
In PyMol I can see this, but when I set the tunnel to sphere in chimeraX, it’s continuously the same diameter.
I can change the colouring to b-factor and here it acknowledges the atom b factor range of 0.8 - 4-8 but I want to visualise the differences.

Please can someone help me with a command?

BW,
Kelly

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