Move model to specific coordinates of reference model
Hi there, I am trying to place a model (volume) at specific coordinates of a second volume (the first model is a map and the second model is a tomogram). I have managed to place a sphere at the desired position, but I can’t figure out how do this with a volume file. Example for placing the sphere: shape sphere radius 100 center 5243.80,3103.88,1086.01 coordinateSystem #1 How can I achieve the same but placing a volume at the desired location? Thanks a lot, Best, Matthias
Hi Matthias, Hmmmm...there are a few possibilities, and it also depends on how you want to define the centers of the map and the tomogram. If you know or can figure out what their centers are, then you can subtract the coordinates of one center from the other and then do exact translations of one model or another along x, y, and/or z using the "move" command, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> - OR - set map grid origin to specific coordinates using the "volume" command "origin" option (or make a certain grid point have coordinates 0,0,0 with "originIndex" option) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions Ways to define the center are as center of grid, or as center of mass. You can get map/tomo center of mass from "measure center" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#center> You could figure out center of grid coordinates given the grid size (number of points in each dimension), origin, and voxel size, which can all be reported with the "volume settings" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#settings> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 18, 2021, at 11:47 AM, Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> wrote:
Hi there, I am trying to place a model (volume) at specific coordinates of a second volume (the first model is a map and the second model is a tomogram). I have managed to place a sphere at the desired position, but I can’t figure out how do this with a volume file.
Example for placing the sphere:
shape sphere radius 100 center 5243.80,3103.88,1086.01 coordinateSystem #1
How can I achieve the same but placing a volume at the desired location? Thanks a lot, Best, Matthias
Hi Elaine, Thanks a lot, this help! __ Best, Matthias On 18.03.21, 21:30, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: Hi Matthias, Hmmmm...there are a few possibilities, and it also depends on how you want to define the centers of the map and the tomogram. If you know or can figure out what their centers are, then you can subtract the coordinates of one center from the other and then do exact translations of one model or another along x, y, and/or z using the "move" command, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> - OR - set map grid origin to specific coordinates using the "volume" command "origin" option (or make a certain grid point have coordinates 0,0,0 with "originIndex" option) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions Ways to define the center are as center of grid, or as center of mass. You can get map/tomo center of mass from "measure center" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#center> You could figure out center of grid coordinates given the grid size (number of points in each dimension), origin, and voxel size, which can all be reported with the "volume settings" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#settings> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 18, 2021, at 11:47 AM, Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> wrote: > > Hi there, > I am trying to place a model (volume) at specific coordinates of a second volume (the first model is a map and the second model is a tomogram). I have managed to place a sphere at the desired position, but I can’t figure out how do this with a volume file. > > Example for placing the sphere: > > shape sphere radius 100 center 5243.80,3103.88,1086.01 coordinateSystem #1 > > How can I achieve the same but placing a volume at the desired location? > Thanks a lot, > Best, > Matthias
participants (2)
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Elaine Meng -
Vorländer,Matthias Kopano