[Chimera-users] [chimera-dev] icosahedron with a T number

[Wei Zhang]

Hi Elaine,

I am able to use hkcage and build a spherical sphere with pentagons and
hexagons. Is there a way to color those pentagons differently?

Thank you,

Wei

On Fri, Apr 10, 2020 at 10:41 AM Wei Zhang <zhangwei at umn.edu> wrote:

> 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 at 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 at 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 at 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
>>
>>
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