The Sketch commands

The Sketch major menu is a menu to draw different stylized pictures of macromolecules. The Sketch menu works similarly to the Draw_mol commands: first an object is opened, by giving it a name. The Sketch_object command is used to do this. Then a series of drawing instructions can be given to add to the currently open sketch object, using the Sketch_add command. Unlike the Zone command, used to draw molecular objects (which are pickable, sketch objects are not), Sketch_add allows you to define the zones by picking start and end residues on the screen. (Of course, you can only do this if you have a molecular object displayed).

The current sketch type is set by the Sketch_type command. The options   available in the current version of O are:

tapeworm

A worm made up of little rectangles in the peptide planes, in the style of Arthur Lesk [12]. Works for protein only, as the atoms forming the peptide plane are needed by the algorithm.  

ribbon

The classic ribbon representation, as described by Carson [1]. A set of cubic b-spline curves is drawn using the central atoms of the molecule atoms as control points. Works for protein molecules only.  

cylinder

This sketch type draws a cylinder, coaxial to an alpha helix. Works for protein molecules only.   The first and last turns in the helix are used to calculate the axis direction of the cylinder.

spiral

The classic alpha-helix style made popular by Jane Richardson [14]. This sketch type is not suited for beta-strand regions, but looks good for RNA structures, when using P or C1* as central atoms.  

arrow

The classic beta-strand style made popular by Jane Richardson. Only suited for protein beta-strand. The arrows do not look good when drawn in alpha-helical regions.  

rattler

Also known as the tube. Draw a smooth looking rattle snake through the central atoms. Very suitable for loop regions of a protein when creating a cartoon.  

The command Sketch_add uses the current definition of what type of sketch you want, and for each type, the characteristic parameters. These parameters are set by Sketch_setup. Normally, once and for all, you would settle for a set of parameters that appeal to you, and only rarely change them. The colours of the sketches are taken from the current colour of the central atom of the molecule. For proteins, this is normally the Ca atom, but the user can define the central atom in the [mol]_molecule_ca datablock. For tRNA, it often looks good to use the C1* atom as the central atom, instead of P. The program can also apply two particular sketch operations to whole objects. These can be used to make objects of balls ( Sketch_cpk) or of sticks ( Sketch_stick). Several different types of sketches can be mixed in the same object. If you begin the definition of a new sketch without defining another object name, the old sketch will be overwritten. A

• Sketch_setup
• Sketch_object
• Sketch_type
• Sketch_add
• Sketch_undo
• Sketch_auto
• Sketch_stick
• Sketch_cpk
• Example
• A note on solid surfaces