# Morph Map

February 15, 2007

This tool linearly interpolates pointwise between two volume data sets. It is for comparing two related volumes, typically two conformations of a structure. It can create an animation showing a smooth progression from one map to another.

## Use

The morph map dialog is displayed using menu entry

      Tools / Volume Data / Morph Map

Open the two maps you wish to interpolate using menu entry File / Open on the main Chimera window. Select these as the first and second maps in the morph map dialog. Alternatively the maps can be opened and chosen using the Browse buttons in the morph map dialog. Then press the Play button or move the Fraction slider to see interpolated maps.

The first time an interpolated map is shown for a given first and second map a writable copy of the first map is created and shown in the volume viewer dialog. The threshold level, step size, surface smoothing settings, ..., of that writable copy control how the appearance of the interpolated map.

## Saving an Animation

Press the Record button to create an animation that progresses through interpolation fractions between Movie start and end values (typically 0 and 1) incrementing by step (default 0.1). When the highest value is reached the fraction is decreased using the same step size to return to the beginning. This causes the animation to show the first map change into the second map and then back to the first map for easy looping.

When all the frames have been recorded a save dialog will be shown to select a file format (e.g. Quicktime, MPEG-2, MPEG-4...) choose a file name, and specify a bit rate. The bit rate determines the tradeoff between high visual quality and small file size. A bit rate of 6000 Kbits/sec is typical of DVD movies. Lower rates give poorer quality and smaller file size.

The Play button progresses through fraction values in the same way but begins at the current slider position and does not record a movie.

## Options

Undisplay original maps.
If this option is on then the first and second map are undisplayed whenever the fraction value is changed.

Multiplier for second map X.
If this option is on then a multiplier value is applied to the second map when interpolating. This allows two maps with different normalizations to be interpolated.

Add to first map instead of interpolating.
If this option is on then the fraction is multiplied times the second map and added to the first map. This is not an interpolation, but instead treats the second map as a delta to be applied to the first map. The second map may for example represent a normal mode for illustrating flexibility of the first map.

## Limitations

Same size maps.
The maps are required to have the same size and the same grid spacing (voxel size in volume dialog Features / Origin and Scale). A subregion of the first map can be used, in which case the corresponding subregion of the second map will be used.

## History

February 15, 2007.
Fixed bug where deleting the interpolated volume leads to error messages when trying to interpolate the same two maps in the same Chimera session.

February 14, 2007.
Fixed bug where Record button always saved movie in Quicktime format ignoring format chosen in file save dialog.

February 7, 2007.
Rewritten by Tom Goddard to use its own user interface dialog and emphasize interpolation between maps instead of adding a multiple of one map to another.

December 22, 2006.
Created by Wei Zhang in Pawel Penczek's lab as an extra panel in the standard Chimera volume viewer dialog.