neon (1) - generate a molecular model with solid stick bonds and shadows

NEON(1)

NAME

neon - generate a molecular model with solid stick bonds and shadows

MIDAS COMMAND SYNTAX

Command: neon [ conic options ]

Command: preneon > output_file

DESCRIPTION

Neon works with the MidasPlus package to create solid stick or ball-and-stick representations of molecular models. The currently displayed atoms, their orientation, position and colors are taken from the interactive display of midas(1) using the pdbrun Midas command and are sent to neon. Neon processes the information under the control of parameters set in the neon.dat file (in the current directory) and the output is sent to the Midas utility conic(1) to create the final image. See conic(1) for a detailed description of its command-line options. Neon has three parameters for the depiction of a simplified backbone: a `smooth' tube connecting A-carbons, an intermediate `bent' tube, and a `straight' tube with straight segments connecting A-carbons. Neon has two parameters which create a smooth gradient of color over the the model based on the temperature factors of the atoms. Dashed or solid lines can be drawn between atoms joined by the distance command in midas to illustrate hydrogen bonds and other interactions. Neon handles Midas objects, allowing arrows and lines to be displayed.

It is also possible to combine neon and conic rendering styles, or differing types of neon rendering styles. See the PRENEON section and the EXAMPLES.

``Capturing Screen Images'' in Part III of the MidasPlus manual discusses saving, converting, and printing neon images.

EXAMPLE OF THE NEON.DAT CONTROL FILE

This file, neon.dat, is read from the current working directory of midas. The example below lists the default control parameters used when the neon.dat file is missing. Input is free format, one control parameter per line.

     0           |Tubetype           |0=all atoms, 1=smooth, 2=bent, 3=straight|
     3           |Sphere density     |1=rough, 5=high resolution               |
     1           |Dash    flag       |0=no dashes,  1=draw dashes              |
     1           |Object  flag       |0=no objects, 1=draw objects             |
     0           |CPK     flag       |0=normal Render output, 1=CPK output     |
     0.25        |Stick   thickness  |Angstroms                                |
     0.50        |Tube    thickness  |Angstroms                                |
     0.10        |Dash    thickness  |Angstroms                                |
     0.10        |Object  thickness  |Angstroms                                |
     0.04        |Density thickness  |Angstroms                                |
     0           |Atom rendering     |0=stick, 1=ball & stick                  |
     0.25        |Atom size          |Fraction of vdw radius (ball&stick mode) |
     0 0.50      |Depthcue,Percent   |0=n, 1=y; fraction aft intensity         |
     0 0.0 0.0   |B-factor,Range     |0=n, 1=shade to color, 2=rainbow; min-max|
     1.0 1.0 1.0 |B-factor color     |RGB (red, green, blue)                   |
     5           |Number of dashes   |Number drawn between each pair of atoms  |
     1.0 1.0 0.0 |Dash color         |RGB (red, green, blue)                   |
     0.30        |Dash offset        |Dist. from atom to first dash, Angstroms |
     0.40        |Dash/space ratio   |0.0=dots, 0.4=dashes, 1.0=solid line     |
     4.00        |CA conect distance |Angstroms                                |

CONTROL CARDS

Tubetype: Backbone atom representation: all atoms, smooth tube, bent tube, or straight tube. The color of the tube representation corresponds to the color of the A- carbon.

Sphere density: Density of spheres drawn to create sticks, tubes, dashes and objects. A value of 3 is good for most work, 4 is recommended for final full-screen images so that individual spheres are not resolved, and 5 is best for closeups of a small number of residues. Increasing the number slows the calculation. Though the setting 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. Neon permits settings up to 11. Note that each setting above 5 uses double the number of spheres of the next lower setting. Therefore, to minimize wait time, always use the lowest setting that provides a satisfactory image.

Dash flag: Set to 1 to draw lines between between atoms connected by the distance command in Midas. The type of line is under control of dash parameters listed below.

Object flag: Set to 1 to include Midas graphics objects. See ``Non-Molecular Graphics Objects'' in Part III of the MidasPlus User's Manual for details on graphics objects.

CPK Flag: Set to 1 to get the same space-filling representation of atoms obtained with conic with the addition of depthcuing, coloring by temperature factor and the inclusion of graphics objects when the corresponding parameters are set.

Stick thickness: Radius in angstroms of sticks connecting atoms.

Tube thickness: Radius in angstroms of tubes connecting A-carbons.

Dash thickness: Radius in angstroms of dashed lines.

Object thickness: Radius in angstroms of lines and dots in graphics objects.

Density thickness: Radius in angstroms of electron density lines (the density itself is not changed, of course!).

Atom rendering: Controls whether atoms are represented as sticks or balls and sticks.

Atom size: Radius of balls in ball-and-stick mode as a fraction of the van der Waals radius specified by midas.

Depthcue, fraction: The first value turns depthcuing on or off. The second value is the fractional intensity of atoms at the back of the image.

B-factor, range: Control of coloring by temperature factor. The first value controls the coloring type. Type 0 turns the option off, so the model will be colored as displayed. Type 1 creates a gradient of color starting with the B-factor color specified below for atoms with lowest temperature factor to the displayed color for atoms with highest temperature factor. Type 2 creates a gradient of color (blue, magenta, red, orange, yellow) from lowest to highest temperature factor value. The second and third values specify the minimum and maximum temperature factors over which the gradient of color is calculated. Atoms with temperature factors above and below the values are colored yellow and blue respectively. If both values are 0.0, the minimum and maximum values are determined from the displayed atoms.

B-factor color: The RGB (red, green, blue) color of atoms with lowest temperature factor. Used with B-factor coloring type 1.

Number of dashes: Controls the number of dashes drawn between pairs of atoms.

Dash color: The RGB (red, green, blue) color of dashed lines.

Dash offset: Controls the distance in angstroms between the center of atoms and the ends of the dashed lines so that dashes do not bump into the model.

Dash/space ratio: Controls the relative proportions of dash and intervening space. A value of 0.0 gives dots, 0.4 is good for dashed lines, and 1.0 gives a solid line.

CA connect distance: Cutoff distance in angstroms for determining if the backbone tube will be drawn between subsequent A- carbons of each model. 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, this parameter is ignored and CONECT records are used to establish connectivity.

RUNNING NEON

A copy of the file /usr/local/midas/resource/neon.dat should be present in your current working directory. Default values will be used if the file is not found.

To create an image, set the desired parameters in neon.dat. In the interactive window of midas, display, orient and color the model or models of interest. Enter the command neon -p to preview the image. After a short pause a small conic window will open displaying the image. Option flags following the neon command correspond to options of conic, which control the appearance of the image and whether the image is saved in a file for later use.

PRENEON

To create a complex image, multiple outputs of neon can be saved, combined, and then sent to conic to draw the final image. The Midas command preneon runs only neon, and the output must be directed to a file. If the output of preneon is not directed to a file it is returned by default to midas, which will have to work its way through many lines of invalid commands. The preneon command does not accept any command line flags.

EXAMPLES

To have a quick look at an image Command: neon -p
To save a full screen image in the file figure.i Command: neon -F -o figure.i
To create a complex image with a ligand shown as sticks and the binding site shown as space-filling atoms, set neon.dat for sticks, display just the ligand and save the output of neon in the file site. Command: preneon > site

Turn on the CPK flag in neon.dat and display just the binding-site atoms. Append the output of neon to the file site. Command: preneon >> site

Send the combined information in the file site to conic using Conic parameters from the file param, and save the full-screen image in the file figure.i. Command: conic -c param -F -o figure.i site

FURTHER EXAMPLES

     The  demonstration  images   included   on   the   MidasPlus
     distribution  CD  show  how to achieve a variety of striking
     effects and give detailed instructions on how each image was
     made.   If these demonstration images have been installed on
     your     system,     they     will     be      found      in
     /usr/local/midas/demos/images.   The README.index file there
     has further information.  If the demonstration  images  have
     not  been  installed  on  your system, you need to mount the
     distribution CD-ROM, and you will find  the  images  in  the
     CD-ROM directory Midas-2.1/demos/images.

FILES

/usr/local/midas/resource/neon.dat - default neon parameter file

AUTHOR

Thomas R. Hynes

Protein Engineering Department, Genentech Inc., and

Department of Pharmaceutical Chemistry, UCSF