Interpolate colors in Morph after Color zone
Hi everyone, Want to make a movie of a movement of a single domain in my complex through morphing through several cryo EM densities. However as it is very complex I wanted to color the domain of interest. I did so with color zone and got a nice result for all the intermediate states. However as soon as I start morphing the color is gone even though interpolate colors is on. Is there are trick to achieve that? I tried segmenting the map and then interpolating through the segmented maps which works in principle fine but I don't really like the edge that is created by the segmentation. Kind regards David Dr. David Haselbach Max-Planck-Institute for biophysical Chemistry Department for structural Dynamics Am Fassberg 11 37077 Germany Tel. +495512011302
Hi David, It may be that you need to color-zone the morph map (not just the input maps), and there is an example in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011343.html> See the first attachment, which is just a short Chimera command script (plain text) despite the mail-system changing its name to something.obj. The second attachment is the resulting movie. I hope this helps, 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 Sep 26, 2016, at 2:00 AM, Haselbach, David <david.haselbach@mpibpc.mpg.de> wrote:
Hi everyone,
Want to make a movie of a movement of a single domain in my complex through morphing through several cryo EM densities. However as it is very complex I wanted to color the domain of interest. I did so with color zone and got a nice result for all the intermediate states. However as soon as I start morphing the color is gone even though interpolate colors is on. Is there are trick to achieve that? I tried segmenting the map and then interpolating through the segmented maps which works in principle fine but I don’t really like the edge that is created by the segmentation.
Kind regards David
Elaine is right. The morph map “interpolate colors” option only handles the case where the maps have a single color. If the maps have multiple colors the morphing is not smart enough to know how the color should be applied to interpolated maps since the interpolation is just linear interpolation of the density values point-wise followed by computing a new contour surface. If you have a structure fit into the maps you can morph the structure with the “Morph Confomations” tool. Then morph both the atomic structure and map at the same time, and color the map to match the structure using color zone to get your domain coloring — the structure does not need to be shown. Tom
On Sep 26, 2016, at 8:56 AM, Elaine Meng wrote:
Hi David, It may be that you need to color-zone the morph map (not just the input maps), and there is an example in this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011343.html>
See the first attachment, which is just a short Chimera command script (plain text) despite the mail-system changing its name to something.obj. The second attachment is the resulting movie.
I hope this helps, 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 Sep 26, 2016, at 2:00 AM, Haselbach, David <david.haselbach@mpibpc.mpg.de> wrote:
Hi everyone,
Want to make a movie of a movement of a single domain in my complex through morphing through several cryo EM densities. However as it is very complex I wanted to color the domain of interest. I did so with color zone and got a nice result for all the intermediate states. However as soon as I start morphing the color is gone even though interpolate colors is on. Is there are trick to achieve that? I tried segmenting the map and then interpolating through the segmented maps which works in principle fine but I don’t really like the edge that is created by the segmentation.
Kind regards David
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participants (3)
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Elaine Meng -
Haselbach, David -
Tom Goddard