Command Reference Set-Structure

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Command Reference: A-C D-H I-P Q-Se Se-St T-Z

Set

Syntax:  set <parameter> {<option>}

The RasMol set command allows the user to alter various internal program parameters such as those controlling rendering options. Each parameter has its own set of permissible parameter options. Typically, omiting the parameter option resets that parameter to its default value. A list of valid parameter names is given below.

Ambient Axes Background BackFade BondMode Bonds BoundBox Cartoon Display FontSize HBonds Hetero HourGlass Hydrogen Kinemage Menus Monitor Mouse Picking Radius Shadow SlabMode Solvent Specular SpecPower SSBonds Stereo Viewing Strands Transparent Gif UnitCell VectPS Write

Show

Syntax:  show information
         show sequence
         show symmetry

The RasMol show command display details of the status of the currently loaded molecule. The command show information lists the molecule's name, classification, PDB code and the number of atoms, chains, groups it contains. If hydrogen bonding, disulfide bridges or secondary structure have been determined, the number of hbonds, ssbonds, helices, ladders and turns are also displayed respectively. The command show sequence lists the residues that comprise each chain of the molecule. The command show symmetry lists the spacegroup and unit cell parameters.

Slab

Syntax:  slab {<boolean>}
         slab <value>

The RasMol slab command enables, disables or positions the z-clipping plane of the molecule. The program only draws those portions of the molecule that are further from the viewer than the slabbing plane. Values range from zero at the very back of the molecule to 100, which is completely in front of the molecule. Intermediate values determine the percentage of the molecule to be drawn.
See set slabmode for additional parameters used in slabbing.

Spacefill

Syntax:  spacefill {<boolean>}
         spacefill temperature
         spacefill user
         spacefill <value>

The RasMol spacefill command is used to represent all of the currently selected atoms as solid spheres. This command is used to produce both union-of-spheres and ball-and-stick models of a molecule. The command, spacefilll true, the default, represents each atom as a sphere of Van der Waal's radius. The command spacefill off turns off the representation of the selected atoms as spheres. A sphere radius may be specified as an integer in RasMol units (1/250th Å) or a value containing a decimal point. A value of 500 (2.0 Å) or greater results in a "Parameter value too large" error.

The temperature option sets the radius of each sphere to the value stored in its temperature field. A zero or negative value causes no change in the selected atom. Temperature values greater than 2.00 are truncated to 2. The user option allows the radius of the selected spheres to be specified by additional lines in the molecule's PDB file using Raster 3D's COLOR record extension.

The RasMol command cpk is synonymous with the spacefill command.

SSBonds

Syntax:  ssbonds {<boolean>}
         ssbonds <value>

The RasMol ssbonds command is used to represent the disulfide bridges of the protein molecule as either dotted lines or cylinders between the connected cysteines. The first time that the ssbonds command is used, the program searches the structure of the protein to find half-cysteine pairs (cysteines whose sulfurs are within 3 Å of each other) and reports the number of bridges to the user. The command ssbonds on displays the selected 'bonds' as dotted lines, and the command ssbonds off disables the display of ssbonds in the currently selected area. Selection of disulfide bridges is identical to normal bonds, and may be adjusted using the RasMol set bondmode command. The color of disulfide bonds may be changed using the color ssbonds command. By default, each disulfide bond has the colors of its connected atoms.

By default disulfide bonds are drawn between the sulfur atoms within the cysteine groups. By using the set ssbonds command, the position of the cysteine's alpha carbons may be used instead.

Stereo

Syntax:  stereo on 
         stereo [-] <number>
         stereo off

The RasMol stereo command provides side-by-side stereo display of images. Stereo viewing of a molecule may be turned on (and off) either by selecting Stereo from the Options menu, or by typing the commands stereo on or stereo off. The separation angle between the two views may be adjusted with the set stereo [-] <number> command, where positive values result in crossed eye viewing and negative values in relaxed (wall-eyed) viewing. The inclusion of [-] <number> in the stereo command, as for example in stereo 3 or stereo -5, also controls angle and direction.

As of RasMol version 2.6-beta-2, the stereo command is only partially implemented. When stereo is turned on, the image is not properly recentered. (This can be done with a translate x -<number> command.) It is not supported in vector PostScript output files; is not saved by the write script command; and in general is not yet properly interfaced with several other features of the program.

Strands

Syntax:  strands {<boolean>}
         strands <value>
         strands dash

The RasMol strands command displays the currently loaded protein or nucleic acid as a smooth "ribbon" of depth-cued curves passing along the backbone of the protein. The ribbon is composed of a number of strands that run parallel to one another along the peptide plane of each residue. The ribbon is drawn between each amino acid whose alpha carbon is currently selected. The color of the ribbon is changed by the RasMol color ribbon command. If the current ribbon color is none (the default), the color is taken from the alpha carbon at each position along its length. The color of the central and outermost strands may be colored independently using the color ribbon1 and color ribbon2 commands respectively. The number of strands in the ribbon may be altered using the RasMol set strands command.

The width of the ribbon at each position is determined by the optional parameter in the usual RasMol units. By default the width of the ribbon is taken from the secondary structure of the protein or a constant value of 720 for nucleic acids (which produces a ribbon 2.88 Å wide). The default width of protein alpha helices and beta sheets is 380 (1.52 Å) and 100 (0.4 Å) for turns and random coil. The secondary structure assignment is either from the PDB file or calculated using the DSSP algorithm as used by the structure command. This command is similar to the RasMol command ribbons which renders the biomolecular ribbon as a smooth shaded surface.

Wireframe, backbone, and strands representations may be displayed with dashed (dotted) lines. This is enabled by allowing the dash or dashes parameter to the wireframe, backbone, and strands commands.

Structure

Syntax:  structure

The RasMol structure command calculates secondary structure assignments for the currently loaded protein. If the original PDB file contained structural assignment records (HELIX and SHEET) these are discarded. Initially, the hydrogen bonds of the current molecule are found, if this hasn't been done already. The secondary structure is then determined using the Kabsch and Sander DSSP algorithm [8]. Once finished, the program reports the number of helices, strands and turns found.

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Command Reference: A-C D-H I-P Q-Se Se-St T-Z