Resample Map Commands

March 13, 2007

This extension adds two new commands newmap and addmaps that enable saving a density map in a rotated orientation by resampling it on a grid in the rotated coordinate frame. This is particularly useful in electron microscope tomography to copy a structure whose symmetry axes are not aligned with the experimental data axes into a map where it is aligned with the axes.

Example Commands

Commands are typed to the Chimera command-line which is displayed using menu entry Favorites / Command-line.

This command creates a new map containing zero values of size 1003 grid points with grid plane spacing equal to 2.4 and origin (i.e. physical xyz position of grid value at index 0,0,0) equal to (-120,-120,-120). An outline box is shown for the new map.

Values from a piece of an experimental map can be copies to the new map. Use the Model Panel dialog (menu entry Favorites / Model Panel) to lock the position of an experimental map (click off its Active button) and then move and rotate the new map with the mouse to the region in the experimental map to be copied. Then use the addmaps command to add the experimental map to the new map.

This adds map with model id number 0 to the one with model id number 1. You can find the model id numbers by looking at the open data sets in Model Panel. This will make a copy of the second map unless it is created with the newmap command or is already a copy of a map. The first map is resampled using trilinear interpolation at the grid points of the second map. It does not modify any files. You can use volume dialog menu entry File / Save Map As... to save the resulting map.


Create a new density map of specified size, grid plane spacing, and origin.

  newmap <xsize> <ysize> <zsize> [<x-spacing> <y-spacing> <z-spacing>] [<x-origin> <y-origin> <z-origin>]

Add one map to a second map, interpolating the first map at the grid points of the second map. A copy of the second map is made if it is not an in-memory map.

  addmaps <map-id-1> <map-id-2>


Map location not remembered.
When a piece of an experimental map is extracted using the addmaps command, the position and orientation of that piece is not remembered in the map file. You can save the new map and then save a Chimera session to keep a record of where the piece belongs in the original map.

Resolution loss.
Resampling a map will result in some loss of resolution. This can be minimized by using smaller grid plane spacing (i.e. pixel size) than the original map.


March 13, 2007. Fixed bug where addmaps did not work if either of the two map arguments were displayed with solid style (volumetric) rendering.

March 9, 2007. Implemented commands newmap and addmaps.