|.rd||Dr. Robert Diamond style files. These are usually in Å 's along the unit cell axes. This style is used by PROTEIN for FC calculations, where the atom type field is used to describe formfactors.|
|.wah||Dr. Wayne Arthur Hendrickson style files as used in PROLSQ.|
|.pdb||the format used at the Protein Data Bank at Brookhaven.|
|.xpl||X-plor style PDB files where column 73 is used as a chain ID.|
|.bud||Furey's PHASES coordinate format.|
|.xyz||FRODO binary files, DSN2 format to some. Only works on Vax/VMS.|
|.o||are binary O database files.|
O > mol m1 c_at a132 c1
O > obj m1sph sph 10 end
O > sel_off
Sel> What molecule [M1 ]:
Sel> Residue range [all molecule]:
O > sel_obj
Sel> Molecular Objects = M1CA M1ALL M1SPH
Sel> Object name: m1sph
Sel> Select on or off [on] ?
O > pd_wr
Util> PDB file name: q.pdb
Util> What molecule [M1 ]:
Util> Residue range [all molecule]:
Util> Define cell constants [ 1.00 1.00 1.00 90.00 90.00 90.00]:
Util> Write out only selected atoms? [No]: y
Util> SEGIDs will be written out
Util> Alternates not present
Util> Anis Us not present
Util> Use the B-factor? [Yes]:
Util> Use the occupancy? [Yes]:
Util> 490 atoms written out.
- tapeworm A worm made up of little rectangles in the peptide planes, in the style of Arthur Lesk (1986). 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 (1988). 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.
- spiral The classic a-helix style made popular by Jane Richards. This sketch type is not suited for b-strand regions, but looks good for RNA structures, when using P or C1* as central atoms.
- arrow The classic b-strand style made popular by Jane Richards. Only suited for protein b-strand. The arrows do not look good when drawn in a-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.
- Solid or line mode [solid]
- Width of tapeworm in Å [1.5].
- Width of ribbon in Å [1.5]
- Number of lines in ribbon . This parameter determines how many parallel curves are drawn along the polypeptide chain.
- Number of segments per peptide . This is the number of points that are generated on the curve between successive Ca's. Five segments gives a nice reasonable compromise between a smooth looking curve, and not too many vectors on the display.
- Smoothness . A value of 1 for the smoothness generates a Cardinal spline instead of a b-spline.
- Rendering mode [solid]. For cylinders, the rendering mode can be line, solid or smooth. Both solid and smooth modes generate solid cylinders, but in the former mode the cylinders are built up using polygons.
- Radius [2.5]. This is the approximate radius of an a-helix.
- Number of edges . The number of facets on the polygonal approximation to the cylinder.
- Rendering mode [ solid]. For arrows, this can be line or solid.
- Width of arrow in Å [2.5].
- Thickness of arrow in Å [0.5].
- Width of arrow head in Å [3.75]. This is the width at the base of the arrowhead. The default is actually 1.5 · the width of the arrow.
- Number of segments ns . This parameter determines how each segment of the arrow is subdivided.
- Number of lines on face & side [7 3]. These parameters are used only in line mode. They can be used to give the arrows a solid look.
- Smoothness s . The s parameter determines the degree of interpolation of the central atom curve. This is done in order to give a smooth appearance of the arrow. The number of extra points inserted between two atoms is equal to 2s-1 where s is the smoothness parameter. Each of the 2s-1 segments are then subdivided into the number sub-segments defined by the 'number of segments' parameter ns. The number of polygons drawn depend very heavily on the two parameters s and ns. For picture taking, you might want a very smooth looking sketch, but when speed is important, a more coarse representation will probably do. The total number of polygons used to render an arrow of length N residues is
- 8(N-1) · (2s-1)ns + 5
- Rendering mode [ solid]. For spirals, this can be line or solid.
- Width of spiral in Å [2.5].
- Thickness of spiral in Å [0.5].
- Width of spiral termini in Å [0.5]. This parameter determines how wide the spiral is at the termini, where it normally joins up with other sketch elements.
- Number of segments ns . As for the arrow.
- Number of lines on face & side [7 3]. As for the arrow.
- Smoothness s . As for the arrow.
- The number of polygons used to draw a spiral of length N residues is:
- 8N · (2s-1)ns
- Rendering mode [ solid]. For rattlers, this can be line or solid.
- Radius of rattler [0.5].
- Number of edges ne . This parameter sets the number of facets.
- Smoothness s . As for the arrow.
- Experimenting with the parameters may result in many interesting looking representations.
- In solid rendering mode, the rattler is made up of tiny polygons. There can be quite a large number of polygons forming a rattler, and the performance of the computer my degrade considerably. If the length of the rattler is N, the number of polygons used in the rendering will be:
- 2N (2s-1) ne
- Rendering mode [ generic]. For sticks, this can be line, solid or generic.
- Rendering mode [smooth]. For spheres, this can be line, solid or smooth.
- Thesselation number .
- In solid or line mode, O will generate spheres made of polygons. This is useful when making plots, since the current version of the plotting program oplot can't handle spheres yet. The thesselation number n determines how close an approximation to a sphere is made. The number of polygons is 2 · 4 (n+1) and is thus a vary rapidly growing function.
- Alpha helix: sketch type [spiral], colour [red], template name [ALPHA]
- Beta strand: sketch type [arrow], colour [blue], template name [BETA]
- Loop: sketch type [rattler], colour [yellow], template name .
- Other sketch types that could be chosen instead of the defaults are for example: cylinder for alpha helix, and tapeworm for loop regions. If the special colour 'molecule' is chosen, the sketch will be coloured according to the molecule's colour for each residue.