does anyone know if there is a way to increase the line thickness of the icosahedron cage in the higher-order structures option? Can't seem to figure it out. Thanks in advance. Kristin Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038
Hi Kristin, The simplest approach is to select the icosahedral cage (ctrl-click on it), the use inspection selector (button in lower right corner of graphics window), and change the "line thickness" parameter to the value you want in screen pixels. Some other approaches using commands "shape", "hkcage" and "meshmol" can do the job -- the meshmol command allowing you to make cylindrical edges if you want that: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html Tom -------- Original Message -------- Subject: [Chimera-users] icosahedral cage From: Kristin Parent <kparent@ucsd.edu> To: chimera-users@cgl.ucsf.edu Date: 7/17/09 11:21 AM
does anyone know if there is a way to increase the line thickness of the icosahedron cage in the higher-order structures option? Can't seem to figure it out. Thanks in advance. Kristin
Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Kristin, My reply mainly echoes Tom's but I'm sending it anyway. 8-) Although that tool doesn't have a specific control for linewidth, you can do it by: (1) selecting the icosahedron mesh (Ctrl-click on it) (2) opening the Selection Inspector (click on the greenish button near the lower right corner of the Chimera window -- may have a magnifying glass on it depending on version -- or, choose "Actions... Inspect" from the menu) (3) in the Selection Inspector, which should be showing "Inspect Surface piece" near the top, change the "line thickness" value near the bottom Even though the lines are fatter, they are still flat (not "sticks"). If you wanted sticks instead of lines, don't bother with the above, and instead use the command "meshmol" to change the mesh surface into sticks: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ meshmol.html> There may be a problem with "meshmol" in the current daily build (I just submitted a bugreport) but it works in the production release, 1.3. The Icosahedron Surface tool generates triangles. There is a related command "hkcage" that shows an icosahedron with pentagons and hexagons, and it includes an option for linewidth: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ hkcage.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 17, 2009, at 11:21 AM, Kristin Parent wrote:
does anyone know if there is a way to increase the line thickness of the icosahedron cage in the higher-order structures option? Can't seem to figure it out. Thanks in advance. Kristin
thank you very much. Kristin
Hi Kristin, My reply mainly echoes Tom's but I'm sending it anyway. 8-)
Although that tool doesn't have a specific control for linewidth, you can do it by:
(1) selecting the icosahedron mesh (Ctrl-click on it)
(2) opening the Selection Inspector (click on the greenish button near the lower right corner of the Chimera window -- may have a magnifying glass on it depending on version -- or, choose "Actions... Inspect" from the menu)
(3) in the Selection Inspector, which should be showing "Inspect Surface piece" near the top, change the "line thickness" value near the bottom
Even though the lines are fatter, they are still flat (not "sticks"). If you wanted sticks instead of lines, don't bother with the above, and instead use the command "meshmol" to change the mesh surface into sticks: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ meshmol.html>
There may be a problem with "meshmol" in the current daily build (I just submitted a bugreport) but it works in the production release, 1.3.
The Icosahedron Surface tool generates triangles. There is a related command "hkcage" that shows an icosahedron with pentagons and hexagons, and it includes an option for linewidth: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ hkcage.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jul 17, 2009, at 11:21 AM, Kristin Parent wrote:
does anyone know if there is a way to increase the line thickness of the icosahedron cage in the higher-order structures option? Can't seem to figure it out. Thanks in advance. Kristin
Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038
participants (3)
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Elaine Meng -
Kristin Parent -
Tom Goddard