Dear Chimera Crew, Is there a way to adjust the transparency of a Z-slice using the Volume Viewer's "planes" feature? Right now, it looks like the Z-slice has transparency and lets you see the isosurfaces/segmentations below it. We would like to turn off the Z-slice transparency so that it blocks everything that is behind it. Such a feature would allow us to use Chimera to make a movie that we've been using Amira for, i.e., a movie in which the isosurface (or segmentation) is "revealed" as the map's Z-slice drops down. If the effect that I'm describing isn't clear, I'd be happy to forward a link to such a movie. Thanks! -Lu -- Lu Gan Postdoc, Jensen Lab Caltech Broad Center, MC 114-96 1200 E. California Blvd. Pasadena, CA 91125 Tel: 626-395-8848 Fax: 626-395-5730
Hi Lu, You can make Chimera plane display opaque. The degree of transparency and brightness are given by the height of the yellow curve on the volume dialog histogram -- at the top of the histogram is completely opaque, and at the bottom is completely transparent. So make the yellow line be entirely at the top of the histogram and set the color of the low (noise) data value nodes in the yellow curve to black. The latest Chimera daily builds have the plane display feature built into the volume dialog. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom
Hi Lu, Here are few more hints for displaying volume data as opaque planes and also some about movie making. As I mentioned before you want the yellow brightness/transparency curve on the volume dialog histogram to be at the top of the histogram. You also want it to extend all the way from the lowest to the highest data value. If the lowest node of the curve does is not at the lowest data value (left edge of histogram) then data values below that lowest node position will not be shown -- so you will be able to see through the plane at those low data values. You may want to add more nodes to the yellow curve. You do this by holding the ctrl key while clicking with the left mouse button on the histogram. Ctrl-click on an existing node will delete nodes too. There is no Chimera command to step through the planes of a volume that would be helpful for making a movie. But it can be done with a little Python code. I've attached the 2 line Python script planes.py that starts and stops plane display. Here's a Chimera command sequence that would make a movie showing 100 planes: cd /location/of/planes/script ; movie record supersample 3 ; open planes.py ; wait 100 ; open planes.py ; movie stop ; movie encode output planes.mov You may want to turn off depth cueing (dimming far objects) to get a brighter plane display. You can use menu entry Tools / Viewing Controls / Effects and switch off depth cueing. There is not a Chimera command to do that. Again a Python script could do it. Or you can setup your scene including depth cueing turned off, save it as a Chimera session and then open that session before running a movie making script. The latest Chimera has a volume command that can be useful for setting initial thresholds, colors, subregion, ... in scripts. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html Tom # ----------------------------------------------------------------------------- # Start or stop volume plane display. Useful for making a movie that steps # through data planes. Example Chimera command sequence to make movie # showing 100 planes. # # cd /location/of/planes/script ; movie record supersample 3 ; open planes.py ; wait 100 ; open planes.py ; movie stop ; movie encode output /tmp/planes.mov # from VolumeViewer.volumedialog import volume_dialog volume_dialog().plane_panel.play_stop_cb()
On Nov 6, 2007, at 9:22 AM, Tom Goddard wrote:
You may want to turn off depth cueing (dimming far objects) to get a brighter plane display. You can use menu entry Tools / Viewing Controls / Effects and switch off depth cueing. There is not a Chimera command to do that. Again a Python script could do it. Or you can setup your scene including depth cueing turned off, save it as a Chimera session and then open that session before running a movie making script.
Hi Lu, I just wanted to mention it is possible to save the depth cueing settings in your preferences file; it is not necessary to save and restart a Chimera session. In the Effects tool mentioned by Tom, you can uncheck "depth cueing" to turn it off, and then click "Save" to save the current settings to the preferences file. Then, later uses of Chimera that refer to the same preferences file will automatically have depth cueing turned off. (the wording is a little weird there because it is possible to have different preferences files in different directories, but if you didn't ever specify a nondefault location, you probably only have one preferences file) Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
participants (4)
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Elaine Meng -
Lu -
Thomas Goddard -
Tom Goddard