icosahedron with a T number
Hello, I have been playing with the icosahedron utility in Chimera. I really like this feature, especially with the sphere factor. The current routine uses a subdivision factor to represent the number of triangles on an icosahedral surface. However this lattice is not the same as we see in icosahedral viruses, which use a T number to designate symmetry. With a subdivision number, there are always hexamers on any edge of the icosahedron, whereas in the virus structure this is not the case. I am wondering if Chimera has an utility that can use the T number as the basis for building an icosahedron surface. Thank you. Hope everything is going well and stay safe! Wei
Hi Wei, Take a look at the "hkcage" command if you want hexagons and pentagons instead of triangles. You give it the h and k values which are related to T number by the equation shown in that page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html> For this kind of question (next time) you probably want the chimera-users@cgl.ucsf.edu mailing list, not chimera-dev which is more for programming questions. Thank you for the good wishes -- you stay safe too! 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 9, 2020, at 4:21 PM, Wei Zhang <zhangwei@umn.edu> wrote:
Hello,
I have been playing with the icosahedron utility in Chimera. I really like this feature, especially with the sphere factor.
The current routine uses a subdivision factor to represent the number of triangles on an icosahedral surface. However this lattice is not the same as we see in icosahedral viruses, which use a T number to designate symmetry. With a subdivision number, there are always hexamers on any edge of the icosahedron, whereas in the virus structure this is not the case.
I am wondering if Chimera has an utility that can use the T number as the basis for building an icosahedron surface.
Thank you.
Hope everything is going well and stay safe!
Wei
Hi Elaine, Thank you for the quick reply and the instructions. I will use the other email address next time. Best regards, Wei On Fri, Apr 10, 2020 at 10:12 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Wei,
Take a look at the "hkcage" command if you want hexagons and pentagons instead of triangles. You give it the h and k values which are related to T number by the equation shown in that page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html>
For this kind of question (next time) you probably want the chimera-users@cgl.ucsf.edu mailing list, not chimera-dev which is more for programming questions.
Thank you for the good wishes -- you stay safe too!
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 9, 2020, at 4:21 PM, Wei Zhang <zhangwei@umn.edu> wrote:
Hello,
I have been playing with the icosahedron utility in Chimera. I really like this feature, especially with the sphere factor.
The current routine uses a subdivision factor to represent the number of triangles on an icosahedral surface. However this lattice is not the same as we see in icosahedral viruses, which use a T number to designate symmetry. With a subdivision number, there are always hexamers on any edge of the icosahedron, whereas in the virus structure this is not the case.
I am wondering if Chimera has an utility that can use the T number as the basis for building an icosahedron surface.
Thank you.
Hope everything is going well and stay safe!
Wei
participants (2)
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Elaine Meng -
Wei Zhang