[chimerax-users] Tunnel visualisation

[Zheng Ruan]

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 at 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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