Hi Richard, Here's a Python script that will make 6 thumbnail images of each map in a directory along +/- x, y and z axes. It sets the map contour level to the mean plus two standard deviations. To use it edit the line that sets the directory where the maps reside. Then start Chimera and open the Python file. Make sure not to cover the Chimera window while it is capturing images. The JPEG image file are placed in the same directory and have names matching the map files with suffixes 1,2,3,4,5,6. Tom # ---------------------------------------------------------------------------- # Make 6 views along +/- xyz axes of each map in a directory. # # Sets image size, background color, silhouette edges, and map contour level. # from chimera import runCommand as run run('windowsize 100 100') # Set image size. run('cd /tmp/emdb') # Go to directory containing maps run('set bg_color white') # White background from chimera import viewer viewer.showSilhouette = True # Turn on silhouette edges import os # Get all files that end with ".map" filenames = os.listdir('.') filenames = [f for f in filenames if f.endswith('.map')] # Create images for f in filenames: run('open %s' % f) # Open map # Set contour level to (mean + two standard deviations) from VolumeViewer import active_volume v = active_volume() m = v.matrix() level = m.mean() + 2*m.std() run('volume #0 level %.6g' % level) # Create 6 map images. fprefix = f.rstrip('.map') # Remove ".map" suffix run('copy file %s_1.jpg jpeg' % fprefix) run('turn y 90') run('copy file %s_2.jpg jpeg' % fprefix) run('turn y 90') run('copy file %s_3.jpg jpeg' % fprefix) run('turn y 90') run('copy file %s_4.jpg jpeg' % fprefix) run('turn y 90') run('turn x 90') run('copy file %s_5.jpg jpeg' % fprefix) run('turn x 180') run('copy file %s_6.jpg jpeg' % fprefix) run('close all')