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<html>
<head>
<title>Using Chemtool</title>
</head>
<body>
<center>
<h1>Using Chemtool</h1>
<h3>1.6.6</h3>
</center>
<p>
Chemtool is a program for drawing organic molecules.
It runs under the X Window System using the GTK widget set.
</p>
<p>
Most operations in chemtool can be accomplished using the mouse - the
first (usually the left) button is used to select or place things, the
middle button modifies properties (e.g. reverses the direction of a bond),
and the right button is used to delete objects.
</p>
<p>
The program offers essentially unlimited undo/redo, two text fonts plus
symbols, seven colors, drawing at several zoom scales, and square and hexagonal backdrop grids
for easier alignment.
</p>
<h2>Drawing of bonds:</h2>
<p>
Bonds can be drawn in 4 different angle settings - hexagon with 30 degree
intervals, two pentagons with 72 degree intervals (in different orientations),
and a 45 degree octagon). Intermediate angles are possible in all of these
modes as well - just ignore the marker points in this case.
</p>
<p>
Pressing the first (left) mouse button sets the starting point of a bond
and also displays a set of markers at the appropriate angular positions.
Dragging the mouse while holding down the button draws a line in the desired
direction.
</p>
<p>
The bond style chooser in the center of the button bar determines the type
of bond that is drawn - initially, this is a single bond. If you want to
change the type of a bond later, either click on it with the middle button
of your mouse to advance to the next type(s), or select the appropriate type
in the chooser and then switch to bondtype mode and pick all bonds that you
want to change over to the new type. Pressing the middle mousebutton on a
bond when in 'Bondtype' mode reverses the direction of that bond.
</p>
<p>
The bond types available in chemtool are
<ul>
<li> a single bond
<li> a double bond (with one line shorter than the other)
<li> a double bond (having the shorter line on the opposite side)
<li> a centered double bond
<li> a triple bond (with the flanking lines shorter than the center)
<li> a wedge-shaped bond
<li> a dashed wedge-shaped bond
<li> a wavy line
<li> a dashed wide line
<li> a half arrow
<li> an arrow
<li> a wide bond
<li> a circle
<li> a dotted line
<li> a single bond that 'cuts out' a segment from any bond it crosses
<li> a triple bond (with equal line lengths)
<li> a quadruple bond
</ul>
The additional bond type available in the pulldown menu,
<ul>
<li>a curved arrow
</ul>
is special insofar as no other bond type can be converted to or from
this type. (it is actually a shortcut for one of the curve-drawing functions
described below).
</p>
<p>
Pressing the third (usually the right) mouse button deletes the bond next
to the cursor position.
</p>
<h3>Semiautomatic drawing of rings:</h3>
<p>
Rings of 3 to 12 members can be drawn easily by holding down the Ctrl key
while drawing a line. This line will then become the first segment of a ring
that is automatically drawn in clockwise direction. The size of the ring
defaults to that appropriate for the selected drawing mode (i.e. 5, 6 or 8
sides), but it can be set on a per-ring basis by pressing Ctlr-<number>
before drawing the ring, where numbers 3-9 correspond to 3 to 9-membered
rings, while 0 to 2 select 10, 11 and 12-membered rings, respectively.
Newly drawn rings can be deleted by pressing Ctrl and mouse button 3 together.
</p>
<h3>Drawing of curved lines:</h3>
<p>
Curved lines for objects like arrows or orbital lobes can be drawn in spline
curve mode by specifing four control points that form a bounding polygon
(startpoint, two points on either side of the peak, endpoint). Of the regular
bondtypes available in the Style menu, the 'single line', 'semiarrow', arrow
and 'dashed line' retain their usual function, while the 'wide line' type
is used to denote a filled polygon. The control points are only visible in
'Move' mode, where they can be dragged around to change the form of a curve
after it is drawn.
</p>
<p>
For drawing curved arrows, there is also a predefined function in the bond
style chooser. This is actually a shortcut for one of the curve drawing
functions described above, with the second and third control points
automatically generated. As such, it can not be converted to or from any
of the conventional bond types.<br>
(One can, however, convert it to any of the other curve types, e.g. to change
the type of arrowhead). The shape of the arrow will usually need to be
adjusted by shifting the control point that appears alongside it in 'Move'
mode.
</p>
<h2>Inserting text:</h2>
<p>
Text written into the text box can be positioned with the cursor and may
appear left, middle or right-aligned in the drawing. The font size can
be selected from the chooser to the right of the text entry field, while
the 't/T' button next to the text-alignment buttons lets you switch between
two fonts - Helvetica for regular labels, and Times Roman for descriptions.
Like the line drawings, text can be in any of the colors available on the
color selector. If you want to change the color, font or alignment of a
label afterwards, just choose the appropriate combination of settings and
then select the desired label with the left mouse button. When the text
entry area is empty, this will just update the properties without changing
the text itself. When the text entry area is not empty, its contents will
also replace the text of the label. Copying the text of a label to the
entry area is done with the middle mouse button, while the right mouse
button deletes the selected label.
</p>
<p>
There are two special characters to be used for sub- and superscripting
the following character:
<p>
'^' to shift up (e.g. N^+ for N<sup>+</sup>)<br>
'_' to shift down (e.g. CH_3 for CH<sub>3</sub>)
</p>
<p>
The control character '|' is used to itializise the following character,
as in |t-Bu (<it>t</it>-Bu), while the '#' character boldfaces it.
</p>
<p>
The special character '@' switches to symbol mode, which uses the standard
X11 symbol font. All alphabetic keys produce the corresponding greek
characters in this mode, and several other symbols are available if their
standard latin1 equivalents are already mapped onto the keyboard:
</p>
<ul>
<table>
<tr><td>latin 1</td><td> </td><td>symbol character</td></tr>
<tr><td>yen sign</td><td> </td><td> infinity</td></tr>
<tr><td>hyphen</td><td> </td><td>up arrow</td></tr>
<tr><td>macron</td><td> </td><td>down arrow</td></tr>
</table>
<p>
The symbols 'plusminus' and 'registered' (trademark) are already in the
standard font, although they are not normally available on the keyboard.
Use the following commands (or add the declarations to your .xmodmaprc )
to make them available via <AltGr>+<Key>
(<RightAlt>+<Key>):
</p>
<pre>
xmodmap -e 'keysym r = r R registered' \
-e 'keysym o = o O yen' \
-e 'keysym p = p P plusminus' \
-e 'keysym u = u U hyphen' \
-e 'keysym d = d D macron'
</pre>
<p
(this leads to AltGr-P = plusminus, AltGr-R = registered in normal mode and
AltGr-O = infinity, AltGr-U = uparrow, AltGr-D = downarrow in symbol font).
</p>
<p>
For 'dots-and-crosses' diagrams, the following mappings to the symbol
font might be useful:<br>
acute -> cross (e.g. keysym x = x X acute)<br>
middle dot -gt; filled dot (e.g. keysym d = d D periodcentered)
(using the degree sign for the open dot).
</p>
<p>
When you want to use symbols as sub- or superscripts, place the sub- or
superscripting character before the '@' character, e.g. K_@a .
</p>
<p>
The right mousebutton can be used to delete text anchored at the cursor
position.
</p>
<h3>Labeling shortcuts:</h3>
<p>
In all bond drawing modes, several keyboard shortcuts are available to
add atom symbols without having to leave drawing mode. The label is placed
at the current drawing position (the endpoint of the last line drawn, or
the spot last clicked on).
</p>
<p>
The keys 'c','h','n','o','s','p' and 'r' insert the corresponding capital
letter, 'l' (lowercase L) inserts 'Cl', while '1', '2', '3' insert CH,CH_2
and CH_3, respectively. The asterisk key (*) inserts a filled circle.
</p>
<p>
Pressing the space bar once allows you to enter arbitrary labels, which will
be placed at the current position when you press the Return key.
</p>
<p>
The keys of the numeric keypad can be used to draw short 'electron pair' lines next to an
element symbol - if one imagines the element symbol to be sitting on the
central '5' key, each key draws the appropriate electron pair for its
position.
</p>
<p>
For quick numbering of the atoms in a molecule, switch to one of the text
modes, hold down the Control key and pick each atom in succession with
the left mouse button. Numbering starts at 1, and the sequence can be reset
at any time by clicking the right mouse button. If you need to use your own
numbering scheme, clicking the middle button (while still holding down the
Control key) makes it pick up whatever number is in the text entry field.
</p>
<h2>Moving, rotating, flipping or scaling objects</h2>
<p>
Using the 'Mark' button, you can easily select parts of the current drawing
by enclosing them with a 'rubberband' rectangle. If you need to add atoms
outside of the rectangular area to your selection, simply draw another
rubberband around them while holding down the Ctrl key.
</p>
<p>
The selected parts will appear highlighted in blue and are immediately
available for
<ul>
<li> moving: simply drag the fragment to the desired position with the mouse
while holding down the left mouse button. Pressing the Ctrl key
limits movement to the horizontal, while pressing the Shift key
selects vertical-only movement.<br>
<b>Note:</b> If you only want to move individual atoms or bonds,
you can simply pick and drag them in 'Move' mode without having to
mark them first.</li>
<li>rotating: horizontal movement of the mouse translates to smooth rotation
around the pivot point selected when pressing the mouse button.
Pressing the Ctrl key switches to stepwise rotation according
to the angular intervals of the current drawing mode.</li>
<li>flipping (mirroring) the fragment about a horizontal or vertical mirror
plane through its center: this is performed by clicking on the appropraite
the menu button</li>
<li>copying : clicking on the 'Copy' menu button creates an exact copy of the
selected fragment slightly offset to the original. The mark is
automatically transfered to the new copy.</li>
<li>rescaling: horizontal mouse movement is translated into a smooth
increase or decrease of size of the marked fragment</li>
<li>deleting : to delete the marked fragment, simply click the third
(usually the right) mouse button after it is highlighted.</li>
<li>optimizing: clicking on the 'bucket and broom' symbol invokes a function
that removes overlapping (duplicate) bonds and labels from
the drawing and tries to straighten bonds that are almost
horizontal or vertical.</li>
<li>bracketing and framing: clicking on the bracket button invokes a pop-up
menu offering a choice of brackets and various boxes. The chosen item
is drawn in the size and position determined by the marker box that was
drawn by the user.</li>
</ul>
<h2>Centering the drawing:</h2>
<p>
If there is not enough space for your molecule you can
put it in the middle of the sheet with the center button.
</p>
<h2>Exporting to foreign formats:</h2>
<p>
You can export your molecules as
<ul>
<li>X bitmap,
<li>encapsulated PostScript (with optional preview image included)
<li>SVG,
<li>XFig,
<li>MDL molfile,
<li>PicTeX.
</ul>
</p>
<p><b>
The PicTeX and Postscript output functions rely on the fig2dev program from the
transfig package.
</b></p>
<p>
You can create the outputs in different sizes according to the current zoom
scale. The PicTeX and Postscript modes additionally allow scaling to an
arbitrary percentage selectable on the export menu .
</p>
<p>
To include the PicTeX-file in your LaTeX document, you will need the pictex
macro package. Depending on the versions you use, you might also have to load
the 'color' package in the preamble of your LaTeX file.<br>
If you experience 'TeX capacity exceeded' error messages, increase the
extra_mem_bot parameter in your texmf.cnf file (usually located in
/usr/share/texmf/web2c, /usr/local/texmf or /etc/texmf).<br>
Pictex is known for its unusual (by tex standards) memory requirements, and
the standard settings often do not account for this (although you may find a
comment a la 'change this if you use pictex' in the texmf.cnf file).<br>
Something like extra_mem_bot=400000 should not hurt on any moderately modern
system.
</p>
<h2>Printing:</h2>
<p>
Since version 1.5, direct printing of diagrams to a Postscript-capable
printing device (or more typically a print queue running ghostscript)
is possible.</p>
<p>
The paper size, magnification, printer name and the print command to
use (currently either lp or lpr) can be stored in the Configuration Dialog.
</p>
<h2>Adding previously saved figures:</h2>
<p>
To add another molecule from a previously saved chemtool drawing, select
its filename in the dialog window that comes up when you press the 'Add'
button. Marking a file in the dialog automatically displays its contents
in a small preview window.
</p>
<p>
The newly added molecule is automatically made active so that it can be
repositioned as desired. If you want to add it to a predefined position
on another molecule, you can mark that attachment site by left-clicking
on it instead of dragging the marker rectangle. A small green dot will
appear at what is now the reference position for the new part. If you save
molecules with such a marker set, it will in turn define their attachment
site when they are added to another drawing.
</p>
<h2>Adding one of the predefined templates:</h2>
<p>
Choosing 'Templates' from the 'Tools' menu opens a second window with a small
collection of predefined structures.
</p>
<p>
Simply click on the image of the desired molecule to add it to your drawing.
The Template window can be kept open throughout a chemtool session - if it
is hidden by another window, you can move it to the front by clicking the
'Template' button in chemtool again.
</p>
<p>
The data in the template system differ from normal chemtool drawings only by
the fact that they are stored within the program, and in a slightly awkward
format (x and y coordinates listed separately in the source file templates.h).
These are meant to provide a convenient basis set available to all users, but
not individually extendable (you can use the 'Add' function for your own
structures). Please let us know if you want specific molecules added to the
templates - their name or ideally a regular chemtool drawing file is all we
need. (send email to martin@ruby.chemie.uni-freiburg.de)
</p>
<h2>Importing from foreign file formats:</h2>
<p>
Chemtool is able to import files written either in the PDB format originally
used by the Protein Databank (which is now also written by most modeling
packages), or in the molfile (V2000) format developed by MDL Inc. for their
ISIS products.</p>
<p> As both formats can contain 3D information, while chemtool
at least currently does 2D drawing only, the molecule is imported as a
temporary 3D image first, which can be rotated using the mouse (with Z-axis
rotation initiated by pressing the Ctrl key simultaneously with the (left)
mouse button 1). After pressing the Return key, the current orientation is stored
as a 2D projection that can be further edited. All editing commands except
zooming are disabled in 3d mode.
</p>
<p>
The PDB import offers a choice which of the atom symbols to import - you
can either import all labels, only those of non-hydrogen atoms, optionally
omitting any trailing sequence numbers, or no labels at all. Bonds are read
from CONECT records, if present, or guessed from the interatomic distances.
In MDL import mode, C atom labels are automatically suppressed, and bond
types are preserved where possible.
</p>
<p>
If you have a version of the BABEL program installed - either the original
Babel written by Pat Walters or the current OpenBabel effort - chemtool will
automatically offer a menu option for importing from any of the file formats
this supports.
</p>
<h2>Determining sum formula and molecular weight:</h2>
<p>
The distribution contains a helper program,
cht, by Radek Liboska (Prague) to calculate sum formula and (exact) molecular
weight from a chemtool drawing file. It is also available from within chemtool
to calculate these data for the current structure or a marked fragment of
it. Cht can be misled by duplicate bonds ( chemtool does not remove overlapping
bonds, such as they might result from fusing ring systems, automatically), by
reaction arrows and by the 'aromatic ring' symbol, so you should avoid these
and check the plausibility of the generated sum formula where possible.
</p>
<p>
cht recognizes the following commonly used abbreviations:
</p>
<table>
<tr><td>Ac</td><td> C2 H3 O</td><td>Acetyl</td></tr>
<tr><td>Ade</td><td> C5 H4 N5 </td><td> Adeninyl</td></tr>
<tr><td>Bn</td><td> C7 H7 </td><td> Benzyl</td></tr>
<tr><td>Bu</td><td> C4 H9 </td><td> Butyl</td></tr>
<tr><td>Bz</td><td> C7 H5 O</td><td> Benzoyl</td></tr>
<tr><td>BOC</td><td> C5 H9 O2</td><td> Butyloxycarbonyl</td></tr>
<tr><td>CE</td><td> C3 H4 N </td><td> Cyanoethyl</td></tr>
<tr><td>Cyt</td><td> C4 H4 N3 O </td><td> Cytosinyl</td></tr>
<tr><td>DBAM</td><td> C9 H19 N </td><td> Dibutylaminomethylene, biradical</td></tr>
<tr><td>DMAM</td><td> C3 H7 N </td><td> Dimethylaminomethylen, biradical</td></tr>
<tr><td>DMTr</td><td> C21 H19 O2</td><td> Dimethoxytrityl</td></tr>
<tr><td>Et</td><td> C2 H5 </td><td> Ethyl</td></tr>
<tr><td>Gua</td><td> C5 H4 N5 O </td><td> Guaninyl</td></tr>
<tr><td>iBu</td><td> C4 H9 </td><td> iso-Butyl</td></tr>
<tr><td>iPr</td><td> C3 H7 </td><td> iso-Propyl</td></tr>
<tr><td>Me</td><td> C H3 </td><td> Methyl</td></tr>
<tr><td>Ms</td><td> C H3 S O2</td><td> Mesyl</td></tr>
<tr><td>MOC</td><td> C2 H3 O2</td><td> Methoxycarbonyl</td></tr>
<tr><td>MOM</td><td> C2 H5 O</td><td> Methoxymethyl</td></tr>
<tr><td>MMTr</td><td> C20 H16 O</td><td> Monomethoxytrityl</td></tr>
<tr><td>Ph</td><td> C6 H5 </td><td> Phenyl</td></tr>
<tr><td>@F(greek phi)</td><td> C6 H5 </td><td> Phenyl</td></tr>
<tr><td>Pr</td><td> C3 H7 </td><td> Propyl</td></tr>
<tr><td>TBDMS</td><td> C6 H15 Si </td><td> tert-Butyldimethylsilyl</td></tr>
<tr><td>TBDPS</td><td> C16 H19 Si </td><td> tert-Butyldiphenylsilyl</td></tr>
<tr><td>tBu</td><td> C4 H9 </td><td> tert-Butyl</td></tr>
<tr><td>Tf</td><td> C F3 S O2</td><td> Triflyl</td></tr>
<tr><td>Thy</td><td> C5 H5 N2 O2</td><td> Thyminyl</td></tr>
<tr><td>TMS</td><td> C3 H9 Si </td><td> Trimethylsilyl</td></tr>
<tr><td>TMTr</td><td> C22 H22 O3</td><td> Dimethoxytrityl</td></tr>
<tr><td>Tol</td><td> C8 H7 O</td><td> Tolyl</td></tr>
<tr><td>Tr</td><td> C19 H15 </td><td> Trityl</td></tr>
<tr><td>Ts</td><td> C7 H7 S O2</td><td> Tosyl</td></tr>
<tr><td>Ura</td><td> C4 H3 N2 O2</td><td> Uracilyl</td></tr>
<tr><td>Z</td><td> C8 H7 O2</td><td> Benzyloxycarbonyl</td></tr>
</table>
<h2>Drawing functions not available within Chemtool:</h2>
<p>
For features not currently supported by chemtool, like patterns or
general line-drawing functions, getting Brian Smith's XFig
drawing package from www-epb.lbl.gov/xfig is highly recommended.
About the only thing it does not offer is support for 'chemical' linetypes
and drawing angles - which is why chemtool was written as a sort of
companion program. (There will probably be more of the most sorely needed
drawing options added to chemtool over time, but duplicating the more
general-purpose features of xfig seems rather pointless.)
</p>
<h2>Licensing :</h2>
<p>
For license information see the file 'COPYING' in this package, i.e. the
GNU General Public License. This software comes with ABSOLUTELY NO WARRANTY.
</p>
</body>
</html>
|
