Neon Image Example

This is a side example from the Images for Publication tutorial describing the creation of static, shadowed renderings with neon (not available on Windows).

[images shown at 25%; click for full size]

Comparison of glycoside hydrolases from different families. Invertase (family 32) is coral, arabinanase A (family 43) is purple, and levansucrase (family 68) is turquoise. Despite differences in sequence, substrate, and catalytic mechanism, the enzymes have similar overall folds (left) and a set of highly conserved acidic residues in the active site (right).

The structures and positions are the same as in the main Images for Publication tutorial. Starting from the same Chimera session (images.py), the following commands were used:

Command: ~ribbon Command: sel @/display Command: chain @ca Command: ~disp ions Command: disp sel Command: ~sel Command: repr stick

The last command improves the interactive appearance but does not affect images saved with neon.

The neon command calls the external programs neon and conic. Parameters can be set within two separate input files, one for each program. Both of these input files were present in the working directory:

neon.dat contains settings such as tube thickness (used for backbone), stick thickness (used for side chains), tubetype ("curviness" of the backbone), sphere density, and depth-cueing values; these are described in detail in the neon manual page. Even though depth cueing in the interactive graphics window has been turned off, this file specifies it should be used to make the images. To maximize shading with depth, the clipping planes should be positioned to abut the structures fairly closely in front and back. Clipping plane positions can be adjusted in the Side View.
conic.dat contains settings to increase the ambient lighting, smooth jagged edges with antialiasing, and make the background fade from black at the bottom to blue at the top; these are described in detail in the conic manual page.

To make neon1.tif, the saved position overall was restored:

Command: reset overall Command: neon -c conic.dat -x 1050 -y 890 -o neon1.tif -s

(Depending on the system, this may take several minutes to complete.) The command-line flags are explained in the conic manual page; -c indicates the file with conic parameters, -x and -y indicate the pixel dimensions of the output image, -o indicates the output file name, and -s indicates that the image should be shown on the screen when the computation is complete. The -s flag works only on Linux, Mac, and SGI systems, and not all image formats can be displayed on all systems. On SGI systems, -f tiff would also be needed to specify TIFF output.

After the saved position closeup was restored and clipping planes were again adjusted to abut the structures, the same command (except for the output file name) was used to generate neon2.tif.

meng@cgl.ucsf.edu / January 2008