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    <h1 id="top">XMakemol Documentation</h1>

    <!-- Page published by Emacs Wiki begins here -->
<h2>Matthew P. Hodges</h2>

<h3>Version: 5.16</h3>

<h2>Overview</h2>

<p>
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 <a href="http://www.lesstif.org">LessTif</a>
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
<a href="http://www.gnu.org/copyleft/gpl.html">http://www.gnu.org/copyleft/gpl.html</a>.

</p>

<p>
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.

</p>

<p>
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.

</p>

<h2>Invocation</h2>

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

</p>

<pre class="example"> Usage: xmakemol [options]
        -a          Switch off atoms
        -b          Switch off bonds
        -h          Switch on hydrogen bonds
        -c &lt;colour&gt; Set the canvas colour
        -e &lt;colour&gt; Set the bounding box colour
        -f &lt;file&gt;   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
</pre>

<p>
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.

</p>

<h2>Menus</h2>

<h3>File</h3>

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

</p>

<h4>Open</h4>

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

</p>

<pre class="example"> 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
</pre>

<p>
The file is set into &ldquo;frames&rdquo; 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.

</p>

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

</p>

<pre class="example"> 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
</pre>

<p>
and ellipses:

</p>

<pre class="example"> 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
</pre>

<p>
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.

</p>

<h4>Revert</h4>

<p>
Revert to the saved version of the current file.

</p>

<h4>Save</h4>

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

</p>

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

<h4>Merge</h4>

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

</p>

<ul>
<li>Use first frame: merge the first frame in the selected file with
   each of those in the current file.
</li>
<li>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.
</li>
</ul>

<h4>Export</h4>

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

</p>

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

<p>
The following options are available for the OpenGL rendering:

</p>

<ul>
<li>GL2PS (EPS): encapsulated PostScript rendering of the canvas
   (uses the <a href="http://www.geuz.org/gl2ps/">GL2PS</a> library).
</li>
<li>GL2PS (PDF): PDF format rendering of the canvas (uses the <a href="http://www.geuz.org/gl2ps/">GL2PS</a>
   library).
</li>
<li>GL2PS (SVG): SVG format rendering of the canvas (uses the <a href="http://www.geuz.org/gl2ps/">GL2PS</a>
   library).
</li>
</ul>

<p>
The following option is available for either type of rendering:

</p>

<ul>
<li>XPM: XPM format rendering of the canvas (only available if XPM
   support has been compiled in).
</li>
</ul>

<h4>Print</h4>

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

</p>

<h4>Quit</h4>

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

</p>

<h3>Control</h3>

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

</p>

<h4>Frames</h4>

<p>
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.

</p>

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

</p>

<ul>
<li>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.
</li>
<li>Stop: stop the animation.
</li>
<li>Next: move to the next frame.
</li>
<li>Previous; move to the previous frame.
</li>
<li>Rewind; move to the first frame.
</li>
<li>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.
</li>
<li>Make anim (XPM only): save an XPM file for each frame, with a
   comment root.
</li>
</ul>

<p>
The speed of the animation can be controlled with the scale bar marked
with &ldquo;Select speed&rdquo;.

</p>

<p>
If the &ldquo;Centre each frame&rdquo; 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.

</p>

<p>
Finally, a frame can be selected by number in the &ldquo;Select frame&rdquo;
text field.

</p>

<h4>Animate</h4>

<p>
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 &ldquo;Start&rdquo; button and can be stopped with the
&ldquo;Stop&rdquo; button. An indication of the progress of the animation is
given in the message area. Such animations can be saved by clicking on
the &ldquo;Save&rdquo; 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.

</p>

<h4>Measure</h4>

<p>
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 &ldquo;Unselect all atoms&rdquo; 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.

</p>

<h4>Perspective</h4>

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

</p>

<h3>Edit</h3>

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

</p>

<h4>Visible</h4>

<p>
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 &ldquo;Toggle H atoms&rdquo;, &ldquo;Invert selection&rdquo;
and &ldquo;Reselect all&rdquo;. Each of these can work for:

</p>

<ul>
<li>all atoms on the canvas.
</li>
<li>all atoms inside a rectangular region.
</li>
<li>all atoms outside a rectangular region.
</li>
</ul>

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

</p>

<p>
If all frames contain the same number of atoms, then the &ldquo;Propagate
visibilities to all frames&rdquo; allows changes to apply to all frames.

</p>

<h4>Positions</h4>

<p>
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.

</p>

<h4>Scale coordinates</h4>

<p>
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.

</p>

<h4>Atom and bond sizes</h4>

<p>
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.

</p>

<h4>Bond factors</h4>

<p>
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 <code>molecule</code> keyword
below), separate factors for intermolecular and intramolecular bonds
can be specified.

</p>

<h4>Vector display</h4>

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

</p>

<h4>Bounding Box</h4>

<p>
With this dialog, the way that the bounding box is determined can be
chosen. If you choose &ldquo;automatically&rdquo;, XMakemol draws a cuboid which
encapsulates all visible atoms. The faces are parallel to the xy, yz
and xz planes. If &ldquo;from file&rdquo; 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.

</p>

<p>
The visibility of the bounding box can be toggled via the &ldquo;Bounding
Box&rdquo; item in the View menu. 

</p>

<p>
This dialog is only available if a file is loaded.

</p>

<h4>Element properties</h4>

<p>
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.

</p>

<h4>GL rendering</h4>

<p>
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.

</p>

<p>
The customizations which can currently be made are:

</p>

<ul>
<li>Switch between &ldquo;No Stereo&rdquo;, &ldquo;Stereo Pair&rdquo; and &ldquo;Red/Blue
   stereo&rdquo; 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.
</li>
<li>Lighting can be switched on and off, and a spotlight effect can be
   added, the diffuseness of which can be customized.
</li>
<li>Molecules can be rendered in the normal &ldquo;Ball and Stick&rdquo; mode or
   as &ldquo;Tubes&rdquo;. In the latter case, bonded atoms are displayed such
   that they appear to cap the bond to which they are attached.
</li>
<li>The number of planes used to represent atom and bond surfaces can
   be altered.
</li>
<li>Options to alter the perspective of the rendered scene (field of
   view, and position of eye).
</li>
</ul>

<h3>Track</h3>

<p>
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.

</p>

<h4>Rotate about local COM</h4>

<p>
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.

</p>

<h4>Rotate about origin</h4>

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

</p>

<h4>Centre</h4>

<p>
This moves the centre of mass of the system to the origin.

</p>

<h4>Original orientation</h4>

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

</p>

<h4>Original position</h4>

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

</p>

<h4>Reflect x coordinates</h4>

<p>
Reflects the atomic coordinates about the yz plane.

</p>

<h4>Reflect y coordinates</h4>

<p>
Reflects the atomic coordinates about the xz plane.

</p>

<h4>Reflect z coordinates</h4>

<p>
Reflects the atomic coordinates about the xy plane.

</p>

<h4>Invert through centre</h4>

<p>
Invert all coordinates through the origin.

</p>

<h3>View</h3>

<p>
The View menu controls what is displayed on the canvas.

</p>

<h4>Atoms</h4>

<p>
Toggle whether or not atoms are displayed.

</p>

<h4>Bonds</h4>

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

</p>

<h4>H-bonds</h4>

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

</p>

<h4>Vectors</h4>

<p>
Toggle whether or not vectors are displayed.

</p>

<h4>Atom numbers</h4>

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

</p>

<h4>Atom symbols</h4>

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

</p>

<h4>Axes</h4>

<p>
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)

</p>

<h4>Bounding box</h4>

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

</p>

<h4>Outline</h4>

<p>
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.

</p>

<h3>Help</h3>

<h4>About</h4>

<p>
Displays the version and Copyright information.

</p>

<h4>Documentation</h4>

<p>
Gives a pointer to the online documentation.

</p>

<h4>Mouse</h4>

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

</p>

<h4>Bugs</h4>

<p>
Details how to report bugs.

</p>

<h2>Miscellaneous</h2>

<h3>The elements file</h3>

<p>
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:

</p>

<pre class="example"> ! 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
</pre>

<p>
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.

</p>

<h3>The xmake_anim.pl script</h3>

<p>
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:

</p>

<pre class="example">Usage: xmake_anim.pl [options] prefix
       -c                (clean up files)
       -d &lt;delay&gt;        (in 1/100th seconds)
       -l &lt;no_loops&gt;     (0 for infinite)
       -o &lt;output&gt;
</pre>

<h3>Other input file options</h3>

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

</p>

<ul>
<li>atom_rgb: give RGB values for the atom colour, overriding the
   default.
</li>
<li>atom_color: give colour name for the atom, overriding the default.
</li>
</ul>

<h4>Periodic systems</h4>

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

</p>

<pre class="example">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
</pre>

<p>
Here, a two atom unit cell is defined, and a 5x5x5 slab is defined to
be rendered by the <code>crystal_images</code> keyword. Three vectors are defined
by the <code>crystal_vector</code> 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 <code>crystal_origin</code> keyword.

</p>

<h4>Customized rendering modes</h4>

<p>
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:

</p>

<pre class="example">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
</pre>

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

</p>

<h4>Customized bounding box</h4>

<p>
You can specify a custom bounding box, which can be shown instead of
the automatically-determined one. This is done using the <code>bbox_xyz</code>
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,

</p>

<pre class="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
</pre>

<p>
draws a box around a water molecule. As you can see, <code>bbox_xyz</code> 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 &ldquo;Bounding Box&rdquo; item in the
&ldquo;Edit&rdquo; 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.

</p>

<h4>Specifying molecules</h4>

<p>
The <code>molecule</code> 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.

</p>

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