Re: [Chimera-users] [chimera-dev] icosahedron with a T number
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@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@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
Hi Wei, In the mesh from "hkcage", a pentagon edge might also be a hexagon edge. So there is no option to make hexagons a different color than the pentagons, if that's what you meant, sorry. There is another tool "Cage Builder" (in menu under Tools... Higher-Order Structure) that lets you build up pentagons and hexagons manually. They have separate edges and are automatically different colors from each other, but it may be too difficult to build the whole thing that way. Also, there isn't an option to control the colors of the hexagons and pentagons; the pentagons are always orange and the hexagons blue. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html> Best, Elaine
On Apr 10, 2020, at 9:06 AM, Wei Zhang <zhangwei@umn.edu> wrote:
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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine, Thank you. Yes. I played with the "cage builder" last night and liked it. I was able to build a T=13 lattice manually (h,k=3,1). But it is too difficult for larger h or k values. I think probably i can write a .bild file with a certain object (eg. a sphere) appears at the center of each pentamer to help visualization. Is there a way to write out a file that contains the centers coordinates of each hexagon or pentagon? Thanks! Wei On Fri, Apr 10, 2020 at 3:05 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Wei, In the mesh from "hkcage", a pentagon edge might also be a hexagon edge. So there is no option to make hexagons a different color than the pentagons, if that's what you meant, sorry.
There is another tool "Cage Builder" (in menu under Tools... Higher-Order Structure) that lets you build up pentagons and hexagons manually. They have separate edges and are automatically different colors from each other, but it may be too difficult to build the whole thing that way. Also, there isn't an option to control the colors of the hexagons and pentagons; the pentagons are always orange and the hexagons blue.
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebu...
Best, Elaine
On Apr 10, 2020, at 9:06 AM, Wei Zhang <zhangwei@umn.edu> wrote:
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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Wei, Did you see the Chimera example of using hkcage to color a virus? https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/herpes/herpes.html <https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/herpes/herpes.html> It has a script markhidden.py. I just tried it with commands "hkcage 3 1" and "open ~/Downloads/markhidden.py". That script put markers at all the hexamer and pentamer centers. I made them bigger with "vdwdefine 3 #1". But it also put a bunch of additional undesired markers on the icosahedron edges (where the pentagons and hexagons are folded). I could select by hand (ctrl click, and shift ctrl click) and delete the undesired markers (menu Actions / Atoms / Delete). Another thing I tried is fattening up the mesh lines with "meshmol #0 1" and colored the fattened lines "color orange #2". Then I tried another tool Volume Tracer (Chimera menu Tools / Volume Data / Volume Tracer), selected by hand the vertices of my orange mesh around a hexagon, and used Volume Trace menu Features / Surfaces and pressed the create button to make some color planes for a hexagon and a pentagon. So there are lots of Chimera tools that can help you manually do this stuff, but it is pretty tedious. Tom
On Apr 10, 2020, at 1:16 PM, Wei Zhang <zhangwei@umn.edu> wrote:
Elaine,
Thank you. Yes. I played with the "cage builder" last night and liked it. I was able to build a T=13 lattice manually (h,k=3,1). But it is too difficult for larger h or k values.
I think probably i can write a .bild file with a certain object (eg. a sphere) appears at the center of each pentamer to help visualization.
Is there a way to write out a file that contains the centers coordinates of each hexagon or pentagon?
Thanks!
Wei
On Fri, Apr 10, 2020 at 3:05 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Wei, In the mesh from "hkcage", a pentagon edge might also be a hexagon edge. So there is no option to make hexagons a different color than the pentagons, if that's what you meant, sorry.
There is another tool "Cage Builder" (in menu under Tools... Higher-Order Structure) that lets you build up pentagons and hexagons manually. They have separate edges and are automatically different colors from each other, but it may be too difficult to build the whole thing that way. Also, there isn't an option to control the colors of the hexagons and pentagons; the pentagons are always orange and the hexagons blue.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebu... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html>>
Best, Elaine
On Apr 10, 2020, at 9:06 AM, Wei Zhang <zhangwei@umn.edu <mailto:zhangwei@umn.edu>> wrote:
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@umn.edu <mailto:zhangwei@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@cgl.ucsf.edu <mailto: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 <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 <mailto: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 <mailto: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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Tom, Boy, there is so much to learn from Chimera! I was able to follow the sequence of the commands listed in your email and produce colored facets of a pentagon and a hexagon. Thank you for your help! Wei On Fri, Apr 10, 2020 at 6:50 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Wei,
Did you see the Chimera example of using hkcage to color a virus?
https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/herpes/herpes.html
It has a script markhidden.py. I just tried it with commands "hkcage 3 1" and "open ~/Downloads/markhidden.py". That script put markers at all the hexamer and pentamer centers. I made them bigger with "vdwdefine 3 #1". But it also put a bunch of additional undesired markers on the icosahedron edges (where the pentagons and hexagons are folded). I could select by hand (ctrl click, and shift ctrl click) and delete the undesired markers (menu Actions / Atoms / Delete). Another thing I tried is fattening up the mesh lines with "meshmol #0 1" and colored the fattened lines "color orange #2". Then I tried another tool Volume Tracer (Chimera menu Tools / Volume Data / Volume Tracer), selected by hand the vertices of my orange mesh around a hexagon, and used Volume Trace menu Features / Surfaces and pressed the create button to make some color planes for a hexagon and a pentagon.
So there are lots of Chimera tools that can help you manually do this stuff, but it is pretty tedious.
Tom
On Apr 10, 2020, at 1:16 PM, Wei Zhang <zhangwei@umn.edu> wrote:
Elaine,
Thank you. Yes. I played with the "cage builder" last night and liked it. I was able to build a T=13 lattice manually (h,k=3,1). But it is too difficult for larger h or k values.
I think probably i can write a .bild file with a certain object (eg. a sphere) appears at the center of each pentamer to help visualization.
Is there a way to write out a file that contains the centers coordinates of each hexagon or pentagon?
Thanks!
Wei
On Fri, Apr 10, 2020 at 3:05 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Wei, In the mesh from "hkcage", a pentagon edge might also be a hexagon edge. So there is no option to make hexagons a different color than the pentagons, if that's what you meant, sorry.
There is another tool "Cage Builder" (in menu under Tools... Higher-Order Structure) that lets you build up pentagons and hexagons manually. They have separate edges and are automatically different colors from each other, but it may be too difficult to build the whole thing that way. Also, there isn't an option to control the colors of the hexagons and pentagons; the pentagons are always orange and the hexagons blue.
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebu...
Best, Elaine
On Apr 10, 2020, at 9:06 AM, Wei Zhang <zhangwei@umn.edu> wrote:
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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Tom Goddard -
Wei Zhang