Dear Chimera developer, I was wondering that is there any way that I can use Chimera to do a 2D image contour plot? Do I need some extra plug in or tools? Thanks a lot, Yao ------ Yao Cong, Ph.D. Research Associate, National Center for Macromolecular Imaging, Baylor College of Medicine, One Baylor Plaza, Alkek Building N420-BCM125, Houston, TX 77030 Tel:713-798-6989 Fax:713-798-1625 Email: cong@bcm.edu
Dear Yao, If you mean to show contour lines in a plane of a density map, you can do that with Volume Viewer. Open the density map, and then in Volume Viewer: - show Planes options by choosing "Features... Planes" from the Volume Viewer menu - In the Planes options, choose which axis the plane should be perpendicular to and click "One." This will automatically change style to "solid," but just change it back to "surface" or "mesh." Use the slider or entry area to specify which plane is shown. - Ctrl-click on the histogram to add more contour levels, can assign them different colors - now there are planar "blobs" instead of outlines. To show just the outlines, choose "Features... Surface and Mesh options" from the Volume Viewer menu, and in those options, turn off the bottom one, "Cap high values at box faces." - you may want to change the background color, for example with command: set bg_color white - you can make the contour lines thicker by entering a larger "Mesh line thickness" in the Volume Viewer Surface and Mesh options I attached an example image. I hope this is what you had in mind. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 12, 2010, at 8:51 AM, Yao Cong wrote:
Dear Chimera developer, I was wondering that is there any way that I can use Chimera to do a 2D image contour plot? Do I need some extra plug in or tools? Thanks a lot, Yao
Dear Elaine, You are so helpful, and I was really amazed by how powerful Chimera can be. Many thanks, Yao On Aug 16, 2010, at 5:54 PM, Elaine Meng wrote:
Dear Yao, If you mean to show contour lines in a plane of a density map, you can do that with Volume Viewer. Open the density map, and then in Volume Viewer:
- show Planes options by choosing "Features... Planes" from the Volume Viewer menu
- In the Planes options, choose which axis the plane should be perpendicular to and click "One." This will automatically change style to "solid," but just change it back to "surface" or "mesh." Use the slider or entry area to specify which plane is shown.
- Ctrl-click on the histogram to add more contour levels, can assign them different colors
- now there are planar "blobs" instead of outlines. To show just the outlines, choose "Features... Surface and Mesh options" from the Volume Viewer menu, and in those options, turn off the bottom one, "Cap high values at box faces."
- you may want to change the background color, for example with command: set bg_color white
- you can make the contour lines thicker by entering a larger "Mesh line thickness" in the Volume Viewer Surface and Mesh options
I attached an example image. I hope this is what you had in mind. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 12, 2010, at 8:51 AM, Yao Cong wrote:
Dear Chimera developer, I was wondering that is there any way that I can use Chimera to do a 2D image contour plot? Do I need some extra plug in or tools? Thanks a lot, Yao
<contour.png>
participants (2)
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Elaine Meng -
Yao Cong