PLUTON Manual

The viewpoint of the picture

A great variety of instructions is available for the specification of the viewpoint. By default a minimum overlap instruction is executed. Other instructions allow the view direction to be chosen by the user in terms of crystal or orthogonal axes, in terms of molecular features, by rotation about the plotting axes from a previously defined view, by rotation about any other line or bond from a previously defined view.

CROT (X/Y/Z) (M) (COLOR [off]) (step [3.0] (nstep [100000]))

CROTX will produce a stick model rotating about the horizontal X-axis. CROTYM gives a model rotation about y, anti-clockwise). Bonds may be colored as a functions of the atomtypes at their end-points with the COLOR sub-keyword.

        Example:
        CROTX COLOR

VIEW MIN (rotations)

This produces a minimum overlap view. The view is perpendicular to the least-squares plane through the included atom set as generated for the current molecule list. A VIEW MIN instruction is executed automatically with a PLOT instruction when no previous VIEW instruction was given.

        Example:
        VIEW MIN XR 45

VIEW UNIT (rotations)

This produces a view with XO along XP (horizontal) and YO along YP (vertical), possibly modified with a sequence of rotations. A given orientation may be reconstructed, independent from its history, using the three rotation values that are shown in the lower right corner (xr), the upper left corner (yr) and the lower left corner (zr) with the instruction:

        VIEW UNIT XROT xr YROT yr ZROT zr
        VIEW is equivalent to VIEW UNIT.

VIEW CURRENT (rotations)

This instruction updates the current view matrix. VIEW rotations is equivalent with VIEW CURRENT rotations.

VIEW XO/YO/ZO (rotations)

View along one of the orthogonal axes towards the origin.

VIEW AFACE/BFACE/CFACE (rotations)

For a view along the line from the point (1.0, 0.5, 0.5), (0.5, 1.0, 0.5) or (0.5, 0.5, 1.0) towards the origin (crystal coordinates).

VIEW ALIGN atom-name1 atom-name2 (aru) WITH XP/YP rotations

This causes an automatic ZROT sufficient to bring the projection of the line between the two atoms parallel to the plotting XP (YP) axis. A warning message is issued when the two atoms are superimposed in the current view, so that this instruction is not uniquely defined.

        Example:
        VIEW ALIGN C1 C2 WITH YP

Note: to bring the vector between the atoms atom_name1 and atom_name2 parallel to XP use the instruction VIEW LINE atom_name1 atom_name2 YROT 90

VIEW DIRECTION x y z (rotations)

This defines a view along the line from the point (x,y,z) towards the origin (crystal coordinates). This may be useful for views down the crystal axes for non-orthogonal crystal systems.

VIEW LINE atom-name1 atom-name2 (rotations)

The direction of view is from the first atom to the second.

VIEW BISECT atom-name1 atom-name2 atom-name3 (rotations)

The view is into the angle n1-n2-n3 with n2 deepest in the plot.

VIEW PERP atom-name1 atom-name2 atom-name3 (rotations)

The view is perpendicular to the plane containing the three atoms, seen from the side which makes a clockwise order of the atoms in the plot n1-n2-n3.

VIEW INVERT (rotations)

An inverted image with respect to the current image is obtained with this instruction.

VIEW MATRIX r11,r12, .. ,r33 (rotations)

This option allows direct input of the view rotation matrix (by row), if it has been previously calculated by another program. An error message will be produced by a matrix for which the determinant is not within reasonable rounding errors of +/-1. rotations:

               (XROT xr)(YROT yr)(ZROT zr)(LROT lr x y z)
               (OROT or x y z)(PROT pr x y z)
               (BROT atom_name1 atom_name2 br)

Examples of VIEW instructions:
     VIEW MIN
     VIEW YO
     VIEW AFACE ZROT 15
     VIEW DIRECTION 0.25 0.25 1
     VIEW LINE PT1 BR1
     VIEW BISECT C1 C2 C3
     VIEW PERP N1 CU1 N2
     VIEW LINE C1 C2 ZROT 90 YROT -30
     VIEW CURRENT BROT C1 C2 -45