XMakemol instructions: version 5.0x
Matthew P. Hodges
1 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 Motif
toolkits for the user interface. XMakemol is 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. To my knowledge, no copy of
XMakemol has ever been sold, so you probably obtained it at no cost.
A copy of the license should have been included in the distribution,
in the file COPYING. If not you can download it from
http://www.gnu.org/copyleft/gpl.html.
XMakemol is principally controlled by the mouse using 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.
2 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
-G Switch on GL rendering [If OpenGL support 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. 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 and politely reminds the user that "XMakemol
comes with ABSOLUTELY NO WARRANTY". The -G option switches
on 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, -bg.
3 Menus
The menu entries under File deal with the reading and writing of
files and quitting the application.
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. It used to
be the case (prior to version 4.16) that all frames had to have the
same value of M. This is no longer the case. Note that details of
each type of atom are held in the elements file (see
§ ) 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 0.0 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 (a,
b and g). The convention used for the Euler angles is:
rotation of g about Z; rotation of b about Y;
rotation of a about Z, where X, Y and Z are global
axes.
Choose a file to save to. The following file types are available:
- Fig (b/w): FIG format rendering of the canvas (black and white).
- Fig (colour): FIG format rendering of the canvas (colour).
- 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.
- EPS (b/w): encapsulated PostScript rendering of the canvas
(black and white).
- EPS (col): encapsulated PostScript rendering of the canvas
(colour).
- Auxiliary info: currently this saves information about the
perspective set for each frame.
- XPM: XPM format rendering of the canvas (requires XPM support to
have been compiled in).
Merge the current Cartesian coordinates with those in another file.
This only works for single-frame files.
Convenient dialog to enable printing of PostScript rendering of the
canvas (black and white, or colour).
Quit the application; no offers will be made to save any data under
any circumstances.
3.2 Control
The menu entries under Control provide a number of pop up dialogs for
controlling various aspects of 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.
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.
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 Measure dialog shows the distances and angles between selected
atoms. Atoms are selected and de-selected 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 (see § ) is also
displayed in the dialog.
3.2.4 Perspective
The perspective dialog contains two scale bars which control aspects
of how the atoms are drawn on the canvas. The "Choose 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. Both the scale and depth are
automatically set when a file is read in.
The menu entries under Edit provide a number of pop up dialogs which
can alter both the properties of atoms and bonds.
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.
Rectangular regions can be drawn with Control + [Mouse-1].
Scale bars 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 in § 3.3.1. When an atom is not selected it is
drawn with a cross-hair and its position cannot be changed.
3.3.3 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
§ ) which is read when the first file is opened.
3.3.4 Bond factors
These two scale bars allow some control over which atoms are
considered to be 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.
3.3.5 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.
3.3.6 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.
3.3.7 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 "Mono" and "Red/Blue stereo" viewing. The
latter 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.
- 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 accuracy to which the atoms and bonds represent spheres and
cylinders can be altered.
- Options to alter the perspective of the rendered scene.
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.
3.4.1 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.
3.4.2 Rotate about origin
If this is selected, the mouse on the canvas will control rotations of
the atoms about the global origin.
This moves the centre of mass of the system to the origin.
3.4.4 Reflect x coordinates
Reflects the atomic coordinates about the yz plane. Plus corresponding
options for reflections about the xy and xz planes.
3.4.5 Invert through centre
Invert all coordinates through the origin.
The View menu controls what is displayed on the canvas.
Toggle whether or not atoms are displayed.
Toggle whether or not bonds are displayed. Bonds can be formed between
any two types of atom.
Toggle whether or not hydrogen bonds are displayed. Hydrogen bonds can
be formed between any hydrogen and any non-hydrogen atoms.
Toggle whether or not vectors are displayed.
3.5.5 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.
3.5.6 Atom symbols
Toggle whether or not the atomic symbols are displayed for each atom.
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).
3.5.8 Bounding box
If enabled, a cuboid is drawn which encapsulated all visible atoms.
The faces are parallel to the xy, yz and xz planes.
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.
In particular, no bonds are drawn and this increases the rendering
speed considerably.
Displays the version and Copyright information.
3.6.2 Documentation
Gives a pointer to the online documentation.
This dialog give a list of actions which the mouse has on the canvas.
Details how to report bugs.
4 Miscellaneous
4.1 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.
File translated from
TEX
by
TTH,
version 3.38.
On 23 Jun 2003, 15:17.