Neon creates shadowed stick and ball-and-stick representations of molecules. The currently displayed atoms and their orientation, position and colors are sent from the interactive display to neon by the pdbrun command. Neon processes the information according to parameters in a file named neon.dat in the current directory (if present) and the output is sent to conic to create the final image. See the conic manual page for a detailed description of the command-line options. See below for a detailed description of the parameters in neon.dat.
Neon has three ways of drawing a simplified protein backbone: as a smoothly curved tube connecting alpha-carbons, an intermediate bent tube, or a tube with straight segments connecting alpha-carbons. Atoms can be colored according to temperature factor (B-factor). Dashed or solid lines can be drawn between atoms joined by the distance command.
It is possible to combine neon and conic rendering styles or differing types of neon rendering styles. See the PRENEON and EXAMPLES sections.
Not yet implemented in Chimera neon:
display of nonmolecular objects such as VDW surface dots.
When neon is invoked, a file named neon.dat in the current working directory is read (if present). If no such file is present, defaults are used. This example neon.dat contains the default values; it can be downloaded and edited as desired. The file is free-format, i.e., the parameters can be placed anywhere on their respective lines as long as they precede any comments.
Below are the default values and names of the parameters, in the order in which they occur in neon.dat. More detailed descriptions follow and can be accessed by clicking the parameter names.
| default(s) | parameter name(s) |
|---|---|
| 0 | tubetype |
| 3 | sphere density |
| 1 | dash flag |
| 1 | object flag |
| 0 | CPK flag |
| 0.25 | stick thickness |
| 0.50 | tube thickness |
| 0.10 | dash thickness |
| 0.10 | object thickness |
| 0.04 | density thickness |
| 0 | atom rendering type |
| 0.25 | atom size |
| 0 0.50 | depthcue, fraction |
| 0 0.0 0.0 | B-factor flag, min, max |
| 1.0 1.0 1.0 | B-factor color |
| 5 | number of dashes |
| 1.0 1.0 0.0 | dash color |
| 0.30 | dash offset |
| 0.40 | dash/space ratio |
| 4.00 | CA connect distance |
tubetype
How to show the backbone of a protein: 0 for all atoms (default), 1 for a smooth tube, 2 for a bent tube, or 3 for a straight tube. The color of the tube corresponds to the color of the alpha-carbon.
sphere density
Density of spheres drawn to create sticks, tubes, dashes and objects. A value of 3 (default) is good for most work, 4 is recommended for final full-screen images involving several residues, and 5 is best for closeups of a small number of residues. Increasing the number slows the calculation. Though 5 is sufficient for almost all situations, occasionally when working on a highly scaled-up view or with very thin cylinders a higher setting is required. Settings up to 11 are permitted. Note that each increment above 5 doubles the number of spheres used. To minimize wait time, always use the lowest setting that provides a satisfactory image.
dash flag
Set to 1 (default) or 0 to draw or not draw lines between between atoms connected by the distance command.
object flag
Set to 1 (default) or 0 to include or not include certain nonmolecular objects.
CPK flag
1 indicates a space-filling (CPK) representation of atoms like that obtained with conic. A reason for using this option rather than simply using conic is that neon has additional features such as depthcuing and coloring by temperature factor. The default setting, 0, indicates a stick or ball-and-stick representation (depending on atom rendering type).
stick thickness
Radius in Å of sticks connecting atoms (0.25 default).
tube thickness
Radius in Å of tubes connecting alpha-carbons (0.50 default) when there is a simplified backbone (when tubetype is not set to 0).
dash thickness
Radius in Å of dashed lines (0.10 default).
object thickness
Radius in Å of lines and dots in nonmolecular objects (0.10 default).
density thickness - (no longer used)
Radius in Å of electron density lines (0.04 default). Note that although density rendering is not implemented in Chimera neon, this line must still be present in neon.dat.
atom rendering type
Controls whether molecules are drawn as sticks (0, default) or balls and sticks (1).
atom size
Radius of a ball in ball-and-stick mode ( atom rendering type set to 1) as a fraction of VDW radius (0.25 default).
depthcue, fraction
The first value turns depthcuing on (1) or off (0, default). The second value is the fractional intensity of the rearmost atoms (0.50 default).
B-factor flag, minimum, maximum
Controls coloring by temperature factor (B-factor). The first value indicates how the coloring will be done:0 (default) turns the option off, so that atoms will be colored as displayed.1 creates a gradient of color starting from the B-factor color for the atoms with the lowest temperature factor and ending with the displayed color for the atoms with the highest temperature factor.2 creates a rainbow gradient of color (blue, magenta, red, orange, yellow) from lowest to highest temperature factor.The second and third values specify the minimum and maximum temperature factor values over which the gradient of color is calculated. If both are 0.0 (default), the minimum and maximum B-factors within the set of displayed atoms are used; the B-factors of undisplayed atoms are ignored.
B-factor color
The RGB color of the atoms with the lowest temperature factor when the B-factor flag is set to 1 (1.0 1.0 1.0 default, white).
number of dashes
Controls the number of dashes in a dashed line (5 by default).
dash color
The RGB color of dashed lines (1.0 1.0 0.0 default, yellow).
dash offset
Controls the distance in Å between the center of atoms and the ends of the dashed lines so that dashes do not bump into the model (0.30 default).
dash/space ratio
Controls the relative proportions of dash and intervening space. A value of 0.0 gives dots, 0.4 (default) is good for dashed lines, and 1.0 gives a solid line.
CA connect distance
Cutoff distance in Å for determining if the backbone tube will be drawn between successive alpha-carbons of each model (4.0 default). For example, if residues 1-10 and 30-40 of a model were displayed, the cutoff would be used to find the break between residues 10 and 30. If unwanted breaks occur, this value should be increased. Note that if tubetype is 0 (all backbone atoms shown), this parameter is ignored and CONECT records are used to establish the connectivity.
When the command neon is used from within Chimera, neon processes the molecular data and then sends it, together with any command-line flags, to conic for rendering. To create a complicated image, multiple outputs of preneon, (which runs only the neon step) can be saved, combined, and then sent to conic; see the third example below. Because the command preneon runs only the neon step, command-line flags are not accepted and the output must be directed to a file.
Next, set CPK flag in neon.dat to
1 (for space-filling)
and display just the binding-site atoms without changing the view.
Append the output of preneon to the file named site:
preneon >> site
Send the combined information in the site to conic,
use the conic parameter file param,
and save the full-screen image into figure.tif:
conic -c param -F -o figure.tif site