BON, BONDS

NAME
BON, BONDS - change drawing style for bonds.

SYNOPSIS
BON style
BONDS style

DESCRIPTION
Change drawing style for bonds. Bond style is defined separately from atom style. This command does not affect disulfide bonds: the command SSB should be used for that purpose. Note that there is no separate keyword for curved bonds and sticks (nice style): the bond curvature is defined by the command PROBE .

STYLE	THICKNESS	TYPE
0	Unvisible bonds.	Fixed.
1	A single line.	Fixed.
2	Three lines.	Fixed.
3	Five lines.	Fixed.
4	Seven lines.	Fixed.
5	Nine lines.	Fixed.
nic nice	Curved bonds, conical sticks or cylindrical sticks, depending both on the probe radius and the atomic radii. This bond style is available for the following atomic styles: SMALL, SM2, COVALENT, CO2, SPACEFILL, SP2, BIG and BI2. Do not combine the nice bond style with atomic styles 0, 1, 2, 3, 4, 5, 6, 7, BALL and BA2.	Proportional.

The image below shows all drawing styles for bonds. To reproduce this image, execute the script bonds.script; the file trp.pdb (tryptophan) is required as input.

NICE BONDS
Nice bonds may be curved or straight, cylindrical or conical, depending on probe radius. If this radius is small (like 0.8 angstroms), the bonds will be curved. Probe radius of 10 angstroms will give the straight bonds. If you want to draw the chemical bonds as cylindrical sticks, use the same atomic radius for all atoms and a relatively large probe. The only way to set the same radius for all atoms is to edit the configuration file (.garlicrc). If your atoms are drawn using different radii, the bonds will appear conical. This is one of the things which make garlic different from most other programs: in garlic, sticks are just the special case of nice bonds. Most other programs are capable to draw just simple cylindrical sticks.

The images below shows the same structure (adrenalin) drawn using two different probes: 0.8 angstroms (curved bonds, the left image) and 10 angstroms (conical sticks, the right image). In both cases all atoms were drawn using the small atomic style with enhanced contrast (ATOMS SM2).

probe 0.8	probe 10

EXAMPLES
In this example, four drawing styles for atoms were combined with four different probes. The following drawing styles were used (vertical, from top to bottom): sm2, co2, sp2 and bi2. Probe radii (angstroms, from left to right): 0.25, 0.50, 1.00 and 2.00. A single benzene molecule was used to prepare this image.

NOTES
(1) Unvisible bonds (style 0) are not treated as hidden - they are just invisible.

(2) A good performance and fairly good contrast may be achieved choosing atom drawing style 0 (no pixels) and bond drawing style 2 (line width of three pixels).

(3) The nice bond style is allowed for ordinary covalent bonds and for disulfide bonds, but not for hydrogen bonds.

(4) Remember that the nice bond style works only for the following atomic styles: SMALL, SM2, COVALENT, CO2, SPACEFILL, SP2, BIG and BI2.

RELATED COMMANDS
PRO (PROBE) is used to set the probe radius. ATO (ATOMS) is used to change the drawing style for atoms. SSB is used to change the bond drawing style for disulfide bonds.