How to Create Isopotential Contours, not Surfaces, with Chimera
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
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
Hi Chuck, Chimera does not have a mode that displays line contours in a plane. This is item 90 on the following Chimera feature request web page: http://www.cgl.ucsf.edu/chimera/plans.html Elaine's two suggestions show a very thin section of the contour surface. This has some problems. First if you use the volume planes mode you'll want to turn of the "Cap high values at box faces" option in the volume dialog Surface and Mesh Options panel. The thin slab cuts out thin ribbons from the surface. They tend to look better if you tilt the plane so you are not viewing it face-on. This seems to reduce the places where the ribbon is viewed edge-on and has zero thickness. Also the appearance is greatly improved if you save a super-sampled image -- reducing the jaggedness. Also the directional lighting on the ribbons is unpleasant. You can reduce it's effects by increasing the brightness of the lights with the volume brightness and transparency panel. All this is still a rather unsatisfactory approximation to what you want. I think it would be not too difficult to make a Python script to draw actual contour lines. If the slab techniques don't work well enough for you let me know and I can try to write such a script. Tom Elaine Meng wrote:
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you Elaine and Thomas for the hints. The per-model clipping is not a route I had thought of. I'll give it a try. Cheers, Chuck -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Monday, August 18, 2008 1:29 PM To: Charles Letner, Ph.D. Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] How to Create Isopotential Contours, not Surfaces, with Chimera Hi Chuck, Chimera does not have a mode that displays line contours in a plane. This is item 90 on the following Chimera feature request web page: http://www.cgl.ucsf.edu/chimera/plans.html Elaine's two suggestions show a very thin section of the contour surface. This has some problems. First if you use the volume planes mode you'll want to turn of the "Cap high values at box faces" option in the volume dialog Surface and Mesh Options panel. The thin slab cuts out thin ribbons from the surface. They tend to look better if you tilt the plane so you are not viewing it face-on. This seems to reduce the places where the ribbon is viewed edge-on and has zero thickness. Also the appearance is greatly improved if you save a super-sampled image -- reducing the jaggedness. Also the directional lighting on the ribbons is unpleasant. You can reduce it's effects by increasing the brightness of the lights with the volume brightness and transparency panel. All this is still a rather unsatisfactory approximation to what you want. I think it would be not too difficult to make a Python script to draw actual contour lines. If the slab techniques don't work well enough for you let me know and I can try to write such a script. Tom Elaine Meng wrote:
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.html
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Charles Letner, Ph.D. -
Elaine Meng -
Thomas Goddard