[chimerax-users] Tunnel visualisation

[Elaine Meng]

Hello Kelly,
I don't know what kind of file(s) you are getting from Caver and opening in ChimeraX, so I don't know what steps are required to show the tunnel.  As far as I know, their downloads give choices for Pymol and VMD, but not Chimera or ChimeraX.

If you could provide an example file that would help.  Otherwise, I can only guess.

Are you saying that the tunnel is represented by an atomic model, and for that model, you want to change the atomic VDW radii (used for sphere representation) to to the values given as bfactor in the file?  If so, see this previous post for how to do that:

<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-July/002416.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 19, 2023, at 5:46 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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