xmakemol.txt

XMakemol Documentation

Matthew P. Hodges

Version: 5.16

Overview

XMakemol is an application for the visualization and manipulation of atomic,
molecular, and other chemical systems. It is written in ANSI C and uses the
Xlib library for rendering and also the Xt and LessTif toolkits for the user
interface. XMakemol is only distributed under the GNU GENERAL PUBLIC LICENSE
(Version 2, June 1991) which means that it is free in the sense that you have
the freedom to obtain and modify the source and to redistribute it. A copy of
the license should have been included in the distribution. You can download
view it at http://www.gnu.org/copyleft/gpl.html.

XMakemol is principally a mouse-based application with menus and pop up dialog
boxes with buttons, scrollbars etc. In addition, some dialogs have text fields
which require information to be inputed from the keyboard. The main window of
the application is split into menus at the top, the canvas in the middle and an
area at the bottom in which messages appear.

The manual will cover invocation then all the menu entries then some
miscellaneous features, mainly dealing with the methods of interacting with the
system on the canvas.

Invocation

Various options are available from the command line. These are as follows:

 Usage: xmakemol [options]
        -a          Switch off atoms
        -b          Switch off bonds
        -h          Switch on hydrogen bonds
        -c <colour> Set the canvas colour
        -e <colour> Set the bounding box colour
        -f <file>   Read file on startup (use '-f -' for STDIN)
        -G          Switch off GL rendering [If OpenGL support is compiled in]
        -u          Print usage information
        -v          Print version information

The -a, -b and -h options toggle the default behaviour and as such might be
useful. The -c and -e options allow the user to control the background and
bounding box colours in case the defaults are not liked (these may be named
colours, e.g., "cadet blue", or hex triplets, e.g., "#5F9EA0"). The -f option
allows a file to be specified to be read in on starting the program. The -u
options echos the above text to standard output and the -v option prints the
version and Copyright information. The -G option switches off rendering using
OpenGL primitives, and is only available if support for OpenGL has been
compiled in. As for any X application, other options can be specified, for
example, -geometry.

Menus

File

The menu entries under File deal with the reading and writing of files and
quitting the application.

Open

Choose a file to be read by XMakemol. The file must be in XYZ syntax an example
of which follows:

 4
   1 Energy = -594.0315361957
 Ar      0.86540     -0.41643      2.29667
 Ar     -1.78146     -2.11666      0.23641
 Ar      1.11998     -0.42506     -1.45518
 Ar     -1.52687      1.63520      0.24505
 4
   2 Energy = -594.0315361957
 Ar      0.86540     -0.41643      2.29667
 Ar     -1.78146     -2.11666      0.23641
 Ar      1.11998     -0.42506     -1.45518
 Ar     -1.52687      1.63520      0.24505

The file is set into "frames" of which there are two in the above example. The
structure of each frame is as follows. The first line contains the number of
atoms in the frame (M) and the second line contains a comment, which may be
empty. The next M lines contain the type of atom followed by the three
Cartesian coordinates; the length unit assumed is Angstrom. Note that details
of each type of atom are held in the elements file (see below) which contains
atomic masses radii and specified colours.

In addition to the basic syntax, it is possible to declare vectors (default
maximum of three per atom):

 3
 Water (axes on oxygen displayed using vectors)
 O    0.0  0.0  0.00 atom_vector 1 0 0 atom_vector 0 1 0 atom_vector 0 0 1
 H    0.77 0.0 -0.59
 H   -0.77 0.0 -0.59

and ellipses:

 3
 All ellipses should look the same
 O    -4.0 0.0 0.0 ellipse 1.0 2.0 2.0  0.0 90.0  0.0
 O     0.0 0.0 0.0 ellipse 2.0 1.0 2.0  0.0 90.0 90.0
 O     4.0 0.0 0.0 ellipse 2.0 2.0 1.0  0.0  0.0  0.0

where the ellipse keyword must be followed by three numbers describing the x, y
and z axis dimensions and three Euler angles (alpha, beta and gamma). The
convention used for the Euler angles is: rotation of gamma about Z; rotation of
beta about Y; rotation of alpha about Z, where X, Y and Z are global axes.

Revert

Revert to the saved version of the current file.

Save

Choose a file to save coordinate data to. The following options are available:

  * XYZ (all): the atom types and Cartesian coordinates for all (visible) atoms
    in all frames.
  * XYZ (frame): the atom types and Cartesian coordinates for all (visible)
    atoms in the current frame.
  * XYZ + connectivities (frame): the information for the current frame, plus
    for each atom a list of the other atoms which it is bonded to.
  * Auxiliary info: currently this saves information about the perspective set
    for each frame.

Merge

Merge the current Cartesian coordinates with those in another file. The
following options are available:

  * Use first frame: merge the first frame in the selected file with each of
    those in the current file.
  * Use all frames: merge the the first frame in the selected file with the
    first in the current file, the second with the second, and so on.

Export

Choose a file to export data to. The following options are available for the
non-OpenGL rendering:

  * Fig (b/w): FIG format rendering of the canvas (black and white).
  * Fig (colour): FIG format rendering of the canvas (colour).
  * EPS (b/w): encapsulated PostScript rendering of the canvas (black and
    white).
  * EPS (colour): encapsulated PostScript rendering of the canvas (colour).

The following options are available for the OpenGL rendering:

  * GL2PS (EPS): encapsulated PostScript rendering of the canvas (uses the
    GL2PS library).
  * GL2PS (PDF): PDF format rendering of the canvas (uses the GL2PS library).
  * GL2PS (SVG): SVG format rendering of the canvas (uses the GL2PS library).

The following option is available for either type of rendering:

  * XPM: XPM format rendering of the canvas (only available if XPM support has
    been compiled in).

Print

Convenient dialog to enable printing of PostScript rendering of the canvas
(black and white, or colour).

Quit

Quit the application; no offers will be made to save any data under any
circumstances.

Control

The menu entries under Control provide a number of pop up dialogs for
controlling various aspects of frames.

Frames

The frames dialog controls the animation of multiple-frame files. At the top,
the frame number and corresponding comments are displayed. If the comment is
empty, this is also indicated.

Next, there are a number of buttons which do the following:

  * Start: start the animation (which loops infinitely). While the animation is
    playing only a limited amount of functionality remains. The Stop button can
    of course be pressed and mouse actions on the canvas are mostly supported.
  * Stop: stop the animation.
  * Next: move to the next frame.
  * Previous; move to the previous frame.
  * Rewind; move to the first frame.
  * Bounce; animate the frames but when the last frame is reached, animate them
    in reverse order until the first frame is reached and so on.
  * Make anim (XPM only): save an XPM file for each frame, with a comment root.

The speed of the animation can be controlled with the scale bar marked with
"Select speed".

If the "Centre each frame" button is activated, then when ever the frame is
changed, the centre of mass is moved to the origin. This can be useful if an
animation involved large displacements of the centre of mass resulting in the
atoms leaving the field of view.

Finally, a frame can be selected by number in the "Select frame" text field.

Animate

The animate dialog allows a frame to be rotated by a specified angle by a
specified number of times about a specified axis. The animation is started with
the "Start" button and can be stopped with the "Stop" button. An indication of
the progress of the animation is given in the message area. Such animations can
be saved by clicking on the "Save" button followed by selecting a filename; the
default type is XYZ, which saves the coordinates for each frame of the
animation. With XPM support, an option to save each frame to an XPM file
exists.

Measure

The Measure dialog shows the distances and angles between selected atoms. Atoms
are selected and deselected using [mouse-3] and a selected atom is indicated on
the canvas by being stippled. Up to four atoms can be pushed on to and popped
off the stack. The selections can be cleared using the "Unselect all atoms"
button. Each selected atom is labelled A-D and these labels also appear on the
canvas. The atom number is also displayed in the dialog.

Perspective

The perspective dialog contains two scale bars: the "Alter scale" simply
controls the size at which atoms, bonds and so on are drawn and the "Choose
depth" scale allows the depth of field to be varied. If the "Toggle depth"
button is not activated, then there is no variation in the atom size with
depth. The settings can be chosen to "Act on all frames" or to "Act on current
frame".

Edit

The menu entries under Edit provide a number of pop up dialogs which can alter
both the properties of atoms and bonds.

Visible

From this dialog, the visibility of each atom can be toggled, i.e., you can
directly control whether or not an atom is displayed on the canvas. Individual
atoms can be selected using Shift + [Mouse-3] and all invisible atoms can
(temporarily) be shown with Shift + [Mouse-1]. In addition the visibility of
groups of atoms can be toggled with buttons labelled for example "Toggle H
atoms", "Invert selection" and "Reselect all". Each of these can work for:

  * all atoms on the canvas.
  * all atoms inside a rectangular region.
  * all atoms outside a rectangular region.

(Note that rectangular regions can be drawn with Control + [Mouse-1].)

If all frames contain the same number of atoms, then the "Propagate
visibilities to all frames" allows changes to apply to all frames.

Positions

Scale bars and text widgets are available to translate the selected atoms in
the X, Y and Z directions, and to rotate the selected atoms about the X, Y and
Z axes. As for the selection of the visible atoms, each can be toggled with
Control + [Mouse-3] when the Edit->Positions dialog is open. Groups of atoms
can be selected in the same way as outlined above. When an atom is not selected
it is drawn with a cross-hair (not OpenGL rendering) and its position cannot be
changed.

Scale coordinates

This dialog allows the atom (and vector) coordinates to be scaled by a constant
factor. Internally, the program uses Angstrom for the unit of length, and a
pre-defined Bohr to Angstrom factor is available, allowing convenient
conversion for input files that have the coordinates in Bohr. An Angstrom to
Bohr factor is available for the reverse transformation.

Atom and bond sizes

In this dialog, the size of the atoms and bonds as displayed on the canvas can
be varied. There are scale bars for the atomic radius, the bond width and the
hydrogen bond width. Note that the sizes of the atoms as displayed on the
canvas also depend on the covalent or van der Waals radii as set in the
external elements file (see below) which is read when the first file is opened.

Bond factors

These two scale bars allow some control over which atoms are considered to be
bonded or H-bonded. The algorithm which determines this information from the
Cartesian coordinates uses the sum of the covalent radii of pairs of atoms.
Increasing the default values will lead to more bonds and decreasing the
default value will lead to fewer bonds. If a system is split into molecules
(see the molecule keyword below), separate factors for intermolecular and
intramolecular bonds can be specified.

Vector display

The vector rendering works better with OpenGL rendering, and this is
recommended at present. Some customization of how the vectors look is possible.

Bounding Box

With this dialog, the way that the bounding box is determined can be chosen. If
you choose "automatically", XMakemol draws a cuboid which encapsulates all
visible atoms. The faces are parallel to the xy, yz and xz planes. If "from
file" is chosen, the minimum and maximum coordinates of the bounding box are
read from the input file. The input fields allow you to adjust the size of the
automatic bounding box.

The visibility of the bounding box can be toggled via the "Bounding Box" item
in the View menu.

This dialog is only available if a file is loaded.

Element properties

This dialog allows the convenient editing of the default element properties
(colour, covalent/van der Waals radii). These can be saved, in which case the
changes will be used for future XMakemol sessions.

GL rendering

If OpenGL support has been compiled in, then this dialog will be present.
Firstly, it allows the switching of rendering between the X and OpenGL
primitives. Secondly, it allows the customization of some of the OpenGL
rendering.

The customizations which can currently be made are:

  * Switch between "No Stereo", "Stereo Pair" and "Red/Blue stereo" viewing:
    the first option renders a single image; the second option renders a stereo
    pair of images for eyes-crossed viewing; the last option requires glasses
    with red and blue lenses. It is possible to alter the separation of the two
    images.
  * Lighting can be switched on and off, and a spotlight effect can be added,
    the diffuseness of which can be customized.
  * Molecules can be rendered in the normal "Ball and Stick" mode or as
    "Tubes". In the latter case, bonded atoms are displayed such that they
    appear to cap the bond to which they are attached.
  * The number of planes used to represent atom and bond surfaces can be
    altered.
  * Options to alter the perspective of the rendered scene (field of view, and
    position of eye).

Track

The Track menu controls the behaviour of the mouse on the canvas and also
allows some general transformations to be made to the atomic coordinates. The
current mouse bindings can be found in the Help menu.

Rotate about local COM

If this is selected, the mouse on the canvas will control rotations of the
atoms about the local centre of mass i.e. that defined by the selected atoms.

Rotate about origin

If this is selected, the mouse on the canvas will control rotations of the
atoms about the global origin.

Centre

This moves the centre of mass of the system to the origin.

Original orientation

Restore the original orientation (i.e., realign axes).

Original position

Restore the original position of the atoms (i.e., remove any displacements made
to the centre of mass).

Reflect x coordinates

Reflects the atomic coordinates about the yz plane.

Reflect y coordinates

Reflects the atomic coordinates about the xz plane.

Reflect z coordinates

Reflects the atomic coordinates about the xy plane.

Invert through centre

Invert all coordinates through the origin.

View

The View menu controls what is displayed on the canvas.

Atoms

Toggle whether or not atoms are displayed.

Bonds

Toggle whether or not bonds are displayed. Bonds can be formed between any two
types of atom.

H-bonds

Toggle whether or not hydrogen bonds are displayed. Hydrogen bonds can be
formed between any hydrogen and any non-hydrogen atoms.

Vectors

Toggle whether or not vectors are displayed.

Atom numbers

Toggle whether of not the atom numbers are displayed for each atom. These
correspond to the order in which the atoms were read in.

Atom symbols

Toggle whether or not the atomic symbols are displayed for each atom.

Axes

Toggle whether or not a set of axes (x,y,z) are displayed on the canvas. These
correspond to a local axis set which before any rotations is parallel to the
global axes (X,Y,Z). (not OpenGL rendering)

Bounding box

If enabled, a cuboid is drawn which encapsulates all visible atoms. The faces
are parallel to the xy, yz and xz planes.

Outline

If enabled, this reduces the amount of drawing done on the canvas while the
system is being rotated or translated. This can be useful for large systems for
which the normal interactive response is slow.

Help

About

Displays the version and Copyright information.

Documentation

Gives a pointer to the online documentation.

Mouse

This dialog gives a list of actions which the mouse has on the canvas.

Bugs

Details how to report bugs.

Miscellaneous

The elements file

The elements file is an external file, the location of which must be specified
in the Makefile before building. The head of the elements file (past the
copyright information) looks like this:

 ! Z     Symbol       Mass        Colour          Cov rad         VdW rad
   1     H            1.008       White           0.300           1.000
   2     HE           4.003       Pink            0.310           1.400

The first entry is the atomic number. The second entry is a label corresponding
to what should be written in an input file (note that comparison is not case
sensitive). The third entry is the atomic mass. The fourth entry is the colour
which is used to paint the atom (and bonds) on the canvas. The final two
entries are covalent and van der Waals radii; if there is no van der Waals
radius for a given atom a value of zero should be used.

The xmake_anim.pl script

This script which is distributed with the source can be used to merge a group
of XPM files produced for an animation into a single file:

Usage: xmake_anim.pl [options] prefix
       -c                (clean up files)
       -d <delay>        (in 1/100th seconds)
       -l <no_loops>     (0 for infinite)
       -o <output>

Other input file options

Examples of the XYZ syntax have been given above. The atom_vector and ellipse
keywords have also been described. Several other keywords are available for use
in input files:

  * atom_rgb: give RGB values for the atom colour, overriding the default.
  * atom_color: give colour name for the atom, overriding the default.

Periodic systems

There is limited support for dealing with periodic systems. This example shows
how to use the available features:

2

Na 0.0 0.0 0.0 crystal_origin   0.0 0.0 0.0 crystal_images 5 5 5
Cl 2.5 2.5 2.5 crystal_vector 1 5.0 0.0 0.0 crystal_vector 2 0.0 5.0 0.0 crystal_vector 3 0.0 0.0 5.0

Here, a two atom unit cell is defined, and a 5x5x5 slab is defined to be
rendered by the crystal_images keyword. Three vectors are defined by the
crystal_vector keyword, and these define the cell vectors. If the origin of the
crystal isn't at the origin itself, an offset can be specified with the
crystal_origin keyword.

Customized rendering modes

It is possible to render different groups of atoms with different rendering
modes when OpenGL rendering is in use with lighting switched on. The syntax is:

63
Water molecule inside Buckminster Fullerene
C  1.22650000   0.00000000   3.31450000  render_tube
C  0.37900000   1.16640000   3.31450000

[...]

C  2.33370000  -2.58660000  -0.59480000
O  0.00000000   0.00000000   0.00000000  render_ball_and_stick
H  0.76923955   0.00000000  -0.59357141
H -0.76923955   0.00000000  -0.59357141

where the first 60 atoms will be rendered as "Tubes", and the final three as
"Balls and Sticks". Note, that if this type of input is used, then the
specifications override the normal "Tubes" or "Ball and Stick" choice that can
be made, and these buttons (described above) will have no effect.

Customized bounding box

You can specify a custom bounding box, which can be shown instead of the
automatically-determined one. This is done using the bbox_xyz keyword. It takes
the minimum and maximum coordinates of the bounding box as parameters, in the
following order: xmin, xmax, ymin, ymax, zmin, zmax. For example,

3
Custom bounding box around water molecule
O  0.00000000   0.00000000   0.00000000
H  0.76923955   0.00000000  -0.59357141  bbox_xyz -1.0 1.0 -0.5 0.5 -1.0 0.5
H -0.76923955   0.00000000  -0.59357141

draws a box around a water molecule. As you can see, bbox_xyz does not have to
be associated with the first atom. If this keyword is given in the input file,
the bounding box will automatically be made visible after the file is loaded.
Via the "Bounding Box" item in the "Edit" menu you can select which bounding
box is shown and also modify the size of the automatically-determined one. If
you give the bounding box data in the first frame, it will be reused in all
frames, unless other data is specified. This feature is, for example, useful if
you want to visualize results of computer simulations of bulk systems, with the
bounding box representing your simulation box.

Specifying molecules

The molecule keyword can be used on an input line to signify the start of a new
molecule (this is implied for the first one). At present, the only feature that
exploits this is the choice of separate values for intermolecular and
intramolecular bond and H-bond factors.

-------------------------------------------------------------------------------

Updated: 2007-08-30