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
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@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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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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Elaine Meng -
Kelly May Frain -
Zheng Ruan