Morph Map

Morph Map morphs between two related sets of volume data (maps). The data sets should have the same grids: dimensions, spacing, and numbers of points. Note the command vop resample can be used to make a copy of one map that has the same grid as another. By default, morphing intermediates are generated by linear interpolation. A smooth progression from one map to the other can be displayed and recorded as a movie. See also: Morph Conformations, Volume Series, making movies, the ParM filament tutorial at the Chimera website

There are several ways to start Morph Map, a tool in the Volume Data category (including from the Volume Viewer Tools menu). It is also implemented as the command vop morph.

The First map and Second map should be chosen from the adjacent lists of open volume data sets. If the maps of interest are not already open, the Browse... buttons can be used to locate and open them.

Moving the Fraction slider generates the corresponding interpolated state. The morph is opened as new volume data set, and its display settings (threshold level/color, surface smoothing, etc.) can be adjusted in Volume Viewer. At a fraction of 0.0, the interpolated map is the same as the First map, and at a fraction of 1.0, it is the same as the Second map.

Clicking Options reveals additional settings that can be hidden again by clicking the small button on the right.

• Movie start [f_s] end [f_e] step [increment] - playback/recording setup: f_s (default 0.0) is the smallest fraction to be visited during playback or the movie, f_e (default 1.0) is the largest, and increment (default 0.1) is the change in fraction per frame
• Undisplay original maps - undisplay the endpoint maps whenever the fraction is changed
• Interpolate colors - interpolate map colors; only applies when the maps have the same number of coloring thresholds (contour levels for surface/mesh display, coloring control nodes for solid display)
• Multiplier for second map [factor] - scale the values in the second map by factor before calculating intermediate values
• Adjust threshold for constant volume - automatically adjust the threshold (contour level) to keep the enclosed volume constant
• Add to first map instead of interpolating - instead of linearly interpolating between data values D1 (from the first map) and D2 (from the second):

  D1(1–fraction) + D2(fraction)
  

  calculate intermediate values with:

  D1 + D2(fraction)
  

  This treats the second map as a delta to be applied to the first map. For example, the second map could represent normal mode fluctuations of the first map.

Clicking the Record button in Morph Map opens a dialog with settings for recording a movie:

• movie File name and location
• File type, with choices:
  • H.264 [.mp4]
  • VP8/WebM [.webm]
  • Theora [.ogv]
  • Quicktime [.mov]
  • AVI MSMPEG-4v2 [.avi]
  • MPEG-4 [.mp4]
  • MPEG-2 [.mpg]
  • MPEG-1 [.mpg]
  • WMV2 [.wmv]
  
  
• Encode forward then backward ("roundtrip") (true/false) - whether to include the frames in reverse order as the second half of the movie
• Rendering:
  • Chimera (default) - Chimera rendering, normally offscreen (details...). Images can be supersampled, that is, initially generated at a higher resolution and then sampled down to the final size.
    • Supersample (1x1/2x2/3x3/4x4) - how many pixels to sample in the X and Y dimensions for each pixel in the final saved image; thus, 1x1 corresponds to no supersampling. Higher values increase the smoothness of edges in saved images and increase calculation time with little effect on file size. 3x3 is generally recommended when supersampling is done.
  • POV-Ray - raytrace with POV-Ray. This rendering option is the slowest but includes fancier effects such as high-quality shadows. The POV-Ray Options button opens the corresponding preferences.

• Quality (highest/higher/high/good/medium/fair/low) - higher quality corresponds to higher (variable) playback bit rates and a larger movie file, assuming the same window size and movie frame rate
• Image format - image file format (however, PNG will be used regardless of this setting if raytracing is done):
  • JPEG [.jpeg]
  • PNG [.jpeg]
  • PPM [.jpeg] (default)
• Additional recording options - options are the same as for the command movie record (include only the options, e.g. directory ~/Desktop/images, not the movie record part); if this field is left blank, image frames will be saved with default names in a default location (but normally deleted after movie encoding, depending on the encoding options)
• Additional encoding options - options are the same as for the command movie encode (include only the options, e.g. resetMode keep, not the movie encode part); if this field is left blank, the movie will be encoded to play at 25 frames per second, and image frames will be deleted after the movie has been encoded

Close dismisses the dialog without initiating recording. Image Tips shows the tips on preparing images, and Help opens this manual page in a browser window.