Hi Chuck, While Chimera does not have an option to do exactly what you want (draw isopotential lines in a plane), there are a couple of ways to approximate the effect by showing a thin slice of isopotential surfaces. The main disadvantage of this slice approach relative to true lines are that you must show some finite thickness and different places in the surface are angled differently relative to the slice plane. Where the surface is very perpendicular to the slice plane it may be barely visible, whereas in other areas it may look like a ribbon of the specified thickness. Given that caveat, here are the slicing approaches: (a) Volume Viewer "Planes" feature, which you discovered. Limitations are you can only slice along data axes and must use depth at least 2 planes (at least in my tests), which may be quite thick. (b) Per-Model Clipping (under Tools... Depiction). If slicing rather than true lines is good enough, I think you want to go this route because it affords complete freedom over slab thickness and orientation. (if you were using Volume Viewer planes, first show "All") Start the tool, enable clipping for the ESP map model, turn on slab mode, adjust thickness, and turn on "adjust clipping with mouse" to allow moving/reorienting the slab interactively. Takes a bit of getting used to, but then you can play all day. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model...
I can't think of any way to do the line drawing as opposed to slicing, however. 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 Aug 17, 2008, at 5:47 PM, Charles Letner, Ph.D. wrote:
Hello all, I have a map of electrostatic potentials. Using volume viewer I am able to display the surfaces at any potential value I would like (as well as multiple values by having multiple bars in the volume viewer histogram). Now, I would like to be able to take a slice through that potential surface and see a line associated with a given value of the potential in that slice – call that the contour. I would like to have multiple potential contours, each with a different constant value in that contour (-10 for one contour, -20 for the next, -30 for the third, and so on- call these the iso-potential contours). This would allow the contours of potential to be seen in a single plane.
Seems like I am so close using planes but that just isn’t working. Am I approaching this right and if so any hints would be appreciated? If I am off base with the approach, I sure would appreciate a nudge in the right direction?
Cheers, Chuck