List of commands

Rotate Model

• x:rotatex <num> Rotate <num> degree around x axis.
• y:rotatey <num> Rotate <num> degree around y axis.
• z:rotatez <num> Rotate <num> degree around z axis.
• vw:view <atom1> <atom2> Rotate models to view from atom1 to atom2. [xref] View

You can also rotate the model by dragging mouse with right button.

Shift Model

• sx:shiftx <num> Translate the model <num> angstrom along x axis.
• sy:shifty <num> Translate the model <num> angstrom along y axis.
• s0:shift0 Reset translation
• vw:view <atom1> Translate the model to set the atom1 at the center of the model window.

Atom Selection

• sl:select <atoms>... Select specified atoms
• sl:select inv Invert selection status of atoms.
• cs:clrstack Reset atom Selection

Display atoms, peaks

• fr:fragment <num> Display one of the fragments.
• in:include <atoms>... Display specified atoms.
• om:omit <atoms>... Omit specified atoms.
• pack [<Xmin> <Xmax> <Ymin> <Ymax> <Zmin> <Zmax>] Create packing diagram.
• pack <Range> Create packing diagram in -Range<x<1+Range, ...
• pack2 [<Range>] Remove fragments outside the unit cell. fragments outside -Range<x<1+Range, ... are removed.

Reconstruct Bonds

• db:delbond <atom> <atom> Remove bond
• mb:makebond <atom> <atom> Create bond
• bu:build <atom> Reconstruct fragment

Projection Control

• sc:scale <num> Zoom <num>.
• dp:depth <num> Projection from <num> angstrom in front of gravity center.
• in:include bl display bond length in model window
• in:include cell display unit cell in model window
• st:stereo [<num>] stereo projection. <num> is the distance between the two figures.
• mo:mono stop stereo projection.

Export file / Execute external program

• pl:plot Export a model to a postscript file, or print out a model.
• cv:cavity Export "cavity" data \& control file, execute cavity. (for cavity Version 4.6, 4.7, 5.0 & 5.1
• or:ortep Export "ortep" data file \& execute ortep (for ortep-for-sun) or3:ortep3 Export "ORTEP III" data file \& execute.

Display Information

• xy:xyz Display atom's information. Coordinates, occupancy factor, thermal parameters, and so on.
• bo:bond <atom1 [<atom2> [<atom3> [<atom4>] ] ] Display bond distance, angle and torsion angle.

View Angle Control

List of commands to control the direction of projection. Mainly used to rotate / shift models.

Rotate models

• rotatex <angle>
• x <angle>

• rotatey <angle>
• y <angle>

• rotatez <angle>
• z <angle>

Rotate models around x,y,z axes. Angles are in degree.

• view <atom 1> <atom 2>
• vw <atom 1> <atom 2>

Rotate to view along atom1 to atom2. The atom 1 will be shift to the center of the window. [xref] View

Mouse drag with right button means rotate x,y,z.

Shift the model

By defaults, the origin of the models is the gravity center of the coordinates, and it is identical to the center of the window. You can shift the models using following commands. This means the shift of the origin. coordinates itself will not be not changed.

Commands for model shifts

• shiftx <num>
• sx <num>
• shifty <num>
• sy <num>

These commands shifts the model along x or y axes. The shift(num) is in angstrom.

• view <atom>
• vw <atom>

This command shift the atom to the center of the window. [xref] View

• shift0
• s0

This commands reset the shifts.

You can also shift by dragging with middle button. (both Left and Right button for two button mouse)

view

"view" command can be used in various way. Details of "view" command is explained in this section.

• view <atom>
• vw <atom>

Shift the model to set the atom at the center of model window.

• view <atom 1> <atom 2>
• vw <atom 1> <atom 2>

Rotate the model to view from atom1 to atom2. The atom1 is also centered.

• view <atom1> <atom2> <atom3>
• vw <atom1> <atom2> <atom3>

Rotate the model to view from atom1 to atom2. The atom1 is also centered. The atom3 become the right side of atom1.

Selection of atoms

Most commands accept 'sl' instead of atom name. This means that the command accept the selected atoms. Command menu of bond window uses the selected atom(s).

Commands:

• select <atom(s)>
• sl <atom(s)>

Select <atoms>. It is identical to click the left button of mouse.

• clrstack
• cs

Clear all selection. Atoms are removed from selected atom list.

Display/Omit Atoms and Peaks.

• fragment <fragment number>
• fr <fragment number>

Display one fragments specified by fragment number. The fragment numbers are automatically calculated by "build" command. [xref] Rebuild

• include <atoms and/or elements>
• in <atoms and/or elements>

Display specified atoms/elements. Special name "sl" is used for selected atoms, "cell" for unit cell, "bl" for bond length. "lb" for atom labels. "ll" means 'long label', and atom labels are extended with symmetry operation code. "afix" for the 'AFIX code' used in SHELX.

• omit <atoms/elements>
• om <atoms/elements>

Omit atoms, elements, unit cell and bond length specified by the name from the model window.

Control projection parameters

In this section, commands to control model projection are explained.

• scale <number>
• sc <number>

Rescale the model window by "number". "L" mark at the bottom left corner of model window indicate 1 angstrom scale.

• depth <number>
• dp <number>

Specify the projection distance from the gravity center of the model. 0 is the special value, and was treated from infinity distance. Distance is in angstrom.

• st [<number>]
• stereo [<number>]

Change projection mode to stereo projection. The number specifies the distance between the left and the right figures in angstrom. Default value is 2.5. "scale 0.5" is automatically executed when stereo command is used.

• mo
• mono

Change projection mode from stereo projection to normal projection. "Scale 2" is also applied.

Plot / Export Model

This section describes commands to plot or export for external commands.

• Output to printer.
• Export cavity format data.
• Export ortep format date.

Output to printer

• plot
• pl

Print out current model to the printer. Command to output can be specified using "SVPRINT" environment variable. Default is "lpr". Postscript type printer can be used with UNIX version of "sv". You can use any printers in MSwin environment.

Export files to calculate cavity.

• cavity vw auto vol bond radii grid exec
• cv vw auto vol bond radii grid exec

Export files used by cavity ver. 4 and 5 series. Parameters are described below.

vw: Projection axis. 0 means the current projection axis. auto: Automatic range selection flag. 1: Automatic, 0: Manual vol: Calculate volume flag. 1:Calculate, 0:Don't calculate bond: Plot bonds 1:Plot 0:Don't plot radii: Radius of atom circles. Usually 0. grid: Separation of grid point. Usually 0.1 - 0.2. Smaller than 0.1 is meaningless for most cases. For the fast calculation to check the shape of cavity, 0.5 is convenient. exec: Automatic execution flag for cav4. 1:Execute, 0:Don't

Export ortep file.

• ortep [<R> [<RH> [<SCode> [<ACode> [<ICode> [<HCode>]]]]]]
• or [<R> [<RH> [<SCode> [<ACode> [<ICode> [<HCode>]]]]]]
• ortep3 [<R> [<RH> [<SCode> [<ACode> [<ICode> [<HCode>]]]]]]
• or3 [<R> [<RH> [<SCode> [<ACode> [<ICode> [<HCode>]]]]]]

"or" or "ortep" commands are used to generate ortep-II style file. This file is tuned to use with ortep-for-sun, ortep-II based program with XView GUI. "or" or "ortep3" commands are used to generate ortep-III style file. This is tuned to the original ortep-III program. Only the atoms and bonds you can see in the model window will be exported to the file.

Before using ortep related commands, you should append or delete all the atoms, bonds, labels of atoms, unit cell, and so on that you want.

R: Radius of atoms expect hydrogens. 0(default) means that the thermal parameters are used for radius. RH: Radius of hydrogen atoms. 0(default) means that the thermal parameters are used for radius. SCode: The shape of selected atmos. Specify numbers in 711-715 range. ACode: The shape of anistropic refined unselected atoms. 711-715. ICode: The shape of isotropic refined unselected atoms. 711-715. HCode: The shape of unselected hydrogen atoms. 711-715.

Information of atoms

View information of atom, for example, coordinates, occupancy factor, thermal parameters, bond distances, angles and so on.

• xyz <atom>
• xy <atom>

Display coordinates, occupancy factor, thermal parameters.

• bond <atom> <distance>
• bo <atom> <distance>

Display all atoms in the sphere specified by the parameters. Center of sphere is <atom> and the radius is specified by the second parameter. Distance is in angstrom.

• bond <atom 1> <atom 2> [ <atom 3> [<atom 4>] ]
• bo <atom 1> <atom 2> [ <atom 3> [<atom 4>] ]

Display bond distance, angle, torsion angle specified by atoms. <atom 3> and <atom 4> can be omitted from command line.

Modify model

In this section, the commands to add or remove bonds are explained.

• delbond <atom 1> <atom 2>
• db <atom 1> <atom 2>

Remove bond between the specified atoms. You can use "sl" to specify selected atoms.

• makebond <atom 1> <atom 2>
• mb <atom 1> <atom 2>

Make new bond between atoms. You can use "sl" to specify selected atoms.

• build <atom>
• bu <atom>

(Re)build molecules from the information of bondings and symmetry operations. When the atom is specified, the molecular that includes the specified atom is numbered as "1". The molecular numbers are used with "fragment" commands. If "auto" is specified as <atom>, the information of bonds are reconstruct from the atom radius and coordinates.