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Atom graphics commands

ball-and-stick atom-selection [atom-selection] ;

ras_gdp_balls

Draw small spheres and sticks (cylinders) between the selected atoms if they are closer to each other than the value of the bonddistance parameter.

The atom spheres are rendered in the same way as in the cpk command, except that the radii are 1/4 of the atom radii.

If one atom selection is given, then all sticks between atoms within this selection are drawn.

If two atom selections are given, then only sticks connecting an atom in the first selection with an atom in the second selection are drawn, in the same way as for bonds. No spheres are output for any atoms when two atom selections are given.

The stickradius parameter controls the radius of the sticks (cylinders). The colour of the sticks is taken from the planecolour parameter if the colourparts parameter is off, otherwise the atom colours are used for each half of the sticks.

In the PostScript output mode, the sticktaper parameter controls the perspective effect applied to the stick.

Parameters: atomradius, atomcolour, colourparts, planecolour, stickradius, sticktaper, lighting.

bonds atom-selection [atom-selection] ;

ras_gdp_bonds

Draw lines between the selected atoms if they are closer to each other than the value of the bonddistance parameter. The colour of the lines is given by the parameter linecolour if the parameter colourparts is off, otherwise the atom colours are used.

If one atom selection is given, then all bonds between atoms within this selection are drawn. For those selected atoms that have no bond connecting them to another atom, a cross is drawn instead if the value of the parameter bondcross is non-zero.

If two atom selections are given, then only bonds connecting an atom in the first selection with an atom in the second selection are drawn. This is useful when one single bond distance cutoff is insufficient to give the desired result (for example, the bonds to the Fe atom versus the cross-ring distances in the five-membered rings in heme groups).

Parameters: atomcolour, bondcross, bonddistance, colourparts, depthcue, linecolour, linedash, linewidth, transparency.

cpk atom-selection ;

ras_gdp_cpk

Draw spheres for the atoms in the selection. The colours and radii of the spheres are taken from the current values for each atom (see parameters atomcolour and atomradius).

For PostScript output, the circle around the sphere is affected by the different line parameters and by the depthcue parameter. The spheres are not actually spheres, but disks. They will therefore not overlap entirely correctly.

For OpenGL output, the quality of the sphere tesselation is affected by the segments parameter.

Parameters: atomradius, atomcolour, colourparts, lighting.

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