[chimerax-users] Tunnel visualisation

[Kelly May Frain]

Hi Elaine, Zheng,

Thank you so much for all your input and quick responses.
As suggested, I used the python script in chimeraX and it worked perfectly!

Best wishes,
Kelly





> On 19 Apr 2023, at 17.46, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Thanks, Zheng!
> 
> By the way, if these values are already assigned as bfactor, another way is to use the python method from the previous post, which might be easier:
> 
> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-July/002416.html>
> 
> After that you would still need to set the atom style of the tunnel model to "sphere" to see the radii.
> 
> Elaine
> 
>> On Apr 19, 2023, at 8:32 AM, Zheng Ruan via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> 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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