Coloring an specific area along a morphing serie among several maps
Dear Srs, I made a chimera movie where six different conformations of the same complex are morphed in a sequence, changing on to the next one (the aim is showing a conformational change occurring in a number of steps, in this case the six electron microscopy maps). My complex has an specially flexible domain and I need to highlight this area along the morphing sequence of the six maps. I suppose that this can be done using the markers and color zone options, but I don't know how to implement this orders in the .cmd script of my movie. Thanks in advance for your help. Sincerely, Ana-Lucia ________________________________ Ana Lucia Alvarez Cabrera Unidad de Bioinformática. Lab. B-13 Dept. Estructura de Macromoléculas Centro Nacional de Biotecnología (CSIC) C/ Darwin 3, Campus de Cantoblanco 28049, Madrid, España Tel: (34) 915854510
Hi all, I have a chimera animation (movie) showing a consecutive morphing sequence among six different conformations of the same complex (I am using electron microscopy 3D maps). The complex has two flexible domains which I want to highlight using a different color from the one applied to the rest of the map, and mantain that color during the morphing. How can I do this? Cheers, Ana-Lucia
Dear Ana-Lucia, You would probably need a session with the 6 density maps, as well as a colored marker set previously created for each map. Then, you could use “vop morph” commands to play the map morph, “modeldisp” and “~modeldisp” to show and hide marker sets by their model numbers (since marker sets are implemented as molecule models), and “scolor zone” for coloring zones to match the markers. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone> I am imagining something like showing the first map and its markers and color zones, hiding markers and showing morph 1->2, then showing map 2 and its markers and color zones, hiding markers and showing morph 2->3, etc.. Perhaps you were thinking of showing markers and colors the whole time and having them also morph, but I don’t know if that is possible. Although there is also a “morph” command to morph between sets of atom coordinates, it is meant for use with biopolymer chains (proteins, DNA, RNA) and it may not work for marker sets. If you try, here is a previous post about synchronizing map morphing with atom morphing: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008752.html> As you may know already, there are lots of other things you can do in the script, like rotating, zooming, and showing title text: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#content> 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 Aug 4, 2015, at 12:54 AM, Ana Lucia Alvarez Cabrera <anlualca@yahoo.com> wrote:
Dear Srs,
I made a chimera movie where six different conformations of the same complex are morphed in a sequence, changing on to the next one (the aim is showing a conformational change occurring in a number of steps, in this case the six electron microscopy maps). My complex has an specially flexible domain and I need to highlight this area along the morphing sequence of the six maps. I suppose that this can be done using the markers and color zone options, but I don't know how to implement this orders in the .cmd script of my movie. Thanks in advance for your help.
Sincerely,
Ana-Lucia
Hi Ana-Lucia, You can use a color zone around a marker to color a specific region. It will be harder if that region moves so much that the marker needs to move with it. Here is the simple case with the marker fixed — the attached command script makes an example movie with two maps, resulting movie attached. Tom
On Aug 4, 2015, at 11:57 AM, Elaine Meng wrote:
Dear Ana-Lucia, You would probably need a session with the 6 density maps, as well as a colored marker set previously created for each map. Then, you could use “vop morph” commands to play the map morph, “modeldisp” and “~modeldisp” to show and hide marker sets by their model numbers (since marker sets are implemented as molecule models), and “scolor zone” for coloring zones to match the markers.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
I am imagining something like showing the first map and its markers and color zones, hiding markers and showing morph 1->2, then showing map 2 and its markers and color zones, hiding markers and showing morph 2->3, etc..
Perhaps you were thinking of showing markers and colors the whole time and having them also morph, but I don’t know if that is possible. Although there is also a “morph” command to morph between sets of atom coordinates, it is meant for use with biopolymer chains (proteins, DNA, RNA) and it may not work for marker sets. If you try, here is a previous post about synchronizing map morphing with atom morphing: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008752.html>
As you may know already, there are lots of other things you can do in the script, like rotating, zooming, and showing title text: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#content>
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 Aug 4, 2015, at 12:54 AM, Ana Lucia Alvarez Cabrera wrote:
Dear Srs,
I made a chimera movie where six different conformations of the same complex are morphed in a sequence, changing on to the next one (the aim is showing a conformational change occurring in a number of steps, in this case the six electron microscopy maps). My complex has an specially flexible domain and I need to highlight this area along the morphing sequence of the six maps. I suppose that this can be done using the markers and color zone options, but I don't know how to implement this orders in the .cmd script of my movie. Thanks in advance for your help.
Sincerely,
Ana-Lucia
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participants (3)
-
Ana Lucia Alvarez Cabrera -
Elaine Meng -
Tom Goddard