BON, BONDS

NAME
BON, BONDS - change drawing style for bonds or refresh (reset) bonds.

SYNOPSIS
BON style
BON REF
BONDS style
BONDS REFRESH

DESCRIPTION
Change drawing style for bonds or refresh (reset) bonds. Bond style is defined separately from atom style. If used to set the bond 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 .

REFRESHING (RESETING) BONDS
The commands CREATE, REPLACE and EDIT may sometimes generate bad bonds. The same may happen if you load the structure which contains some bad coordinates (side chains are too close, for example). If you have spotted bad bonds in your structure, do the following:

(1) Use the command EDIT (EDIT CLICK works fine) to move side chains, individual atoms or groups of atoms away from bad position.

(2) Execute the command BONDS REFRESH. The keyword REFRESH was introduced in version 1.5; it is not available in the earlier versions of this program!

(3) Check are there any bad bonds left. If you can see them, repeat the procedure. Please note that after replacing deeply buried small side chain with a large one you may be missing space - neighbors might be too close!

Refreshing of bonds affects ordinary bonds, as well as disulfide and pseudo-bonds. Pseudo-bonds are bonds connecting pseudo-atoms (quarkonium and jellium). Backbone data and dihedral angles will be updated too.

STYLE	THICKNESS	TYPE
0	Invisible bonds.	Fixed width.
1	A single line.	Fixed width.
2	Three lines.	Fixed width.
3	Five lines.	Fixed width.
4	Seven lines.	Fixed width.
5	Nine lines.	Fixed width.
nic nice	Curved bonds, conical sticks or cylindrical sticks, depending both on the bond 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.
sti sticks	Cylindrical sticks. The command BONDS STICKS (short form: BON STI) is the most convenient way to draw bonds as sticks. Default stick radius may be changed by using the command STICKS (short form: STI).	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 the bond 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. It is, however, more convenient to use the command BONDS STICKS (short form: BON STI) to draw cylindrical sticks. The command BONDS STICKS may be combined with the command STICKS, which is used to adjust the stick radius. If your atoms are drawn using different radii (and this is true for most atomic styles), the bonds will appear conical. This is one of the things which make garlic different from most other programs: in garlic, conical 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 bond 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 nice bonds, drawn with four different probe radii. 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) Invisible 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.

(5) The keyword REFRESH is available since version 1.5!

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. STI (STICKS) is used to change the stick radius. BALLS is used to set the ball radius.