1Chemtool(1) General Commands Manual Chemtool(1)
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6 Chemtool Version 1.6.11
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10 chemtool [<filename>]
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14 Chemtool is a program for drawing organic molecules and exporting them
15 as a X bitmap, PNG, PicTeX, Xfig, SVG, SXD, MDL or EPS file. It runs
16 under the X Window System using the GTK widget set.
17 The program offers essentially unlimited undo/redo, two text fonts plus
19 symbols, seven colors, drawing at several zoom scales, and square and
20 hexagonal backdrop grids for easier alignment.
21
24 In all drawing and editing modes, mouse button one (usually the left
25 button) is used to mark or draw objects, while button three (the right
26 button) can be used to delete objects of the current type. The middle
27 button is mainly used in the bond drawing modes where it allows fast
28 changing of bondtypes. Starting with version 1.5, the default storage
29 directory for datafiles, and the filename extension to use, can be
30 saved via a configuration dialog.
31 Drawing of bonds:
33 Bonds can be drawn in 4 different angle settings (hexagon with 30deg.
35 intervals, two pentagons with 72deg. intervals (different orientation),
36 and a 45deg. i octagon). (Intermediate angles are possible in all of
37 these modes as well - just ignore the marker points in this case).
38 The bond style chooser in the center of the button bar determines the
40 type of bond that is drawn - initially, this is a single bond. If you
41 want to change the type of a bond later, either click on it with the
42 middle button of your mouse to advance to the next type(s), or select
43 the appropriate type in the chooser and then switch to bondtype mode
44 and pick all bonds that you want to change over to the new type. (The
45 color used for the bond is updated at the same time if necessary.)
46 Pressing the middle mousebutton on a bond when in 'Bondtype' mode
47 reverses the direction of that bond.
48 Using the third (usually the right) mouse button deletes the bond next
50 to the cursor position.
51 The available bond types are :
53 single bond
55 double bond
57 double bond (shorter line on the other side)
59 centered double bond
61 triple bond (flanking lines shorter than central)
63 triple bond (with equal line lengths)
65 quadruple bond
67 wedge-shaped bond
69 dashed wedge-shaped bond
71 wavy line
73 half arrow
75 regular arrow
77 wide bond
79 circle
81 dotted line
83 overlapping single bond (which cuts out a segment from any bond it
85 crosses)
86 light pi orbital lobe
88 dark pi orbital lobe
90 Semiaumomatic drawing of rings:
93 Rings of 3 to 12 members can be drawn easily by holding down the Ctrl
95 key while drawing a line. This line will then become the first segment
96 of a ring that is automatically drawn in clockwise direction. The size
97 of the ring defaults to that appropriate for the selected drawing mode
98 (i.e. 5, 6 or 8 sides), but it can be set on a per-ring basis by press‐
99 ing Ctlr-<number> before drawing the ring, where numbers 3-9 correspond
100 to 3 to 9-membered rings, while 0 to 2 select 10, 11 and 12-membered
101 rings, respectively.
102 Newly drawn rings can be deleted by pressing Ctrl and mouse button 3
104 together.
105 Drawing of curved lines:
107 Curved lines for objects like arrows or orbital lobes can be drawn in
109 spline curve mode by specifing four control points that form a bounding
110 polygon (startpoint, two points on either side of the peak, endpoint).
111 Of the regular bondtypes available in the Style menu, the 'single
112 line', 'semiarrow', arrow and 'dashed line' retain their usual func‐
113 tion, while the 'wide line' type is used to denote a filled polygon.
114 The control points are only visible in Move mode, where they can be
115 dragged around to change the form of a curve after it is drawn.
116 Setting bond style:
118 In bond style mode, clicking on any bond in the diagram changes its
120 representation to the type selected in the pull-down menu next to the
121 Type button.
122 The additional bond type available in the pulldown menu,
124 curved arrow
126 is only available for drawing. It is actually a shortcut for one of the
128 curve drawing functions described above, with the second and third con‐
129 trol points automatically generated. As such, it can not be converted
130 to or from any of the conventional bond types.
131 (One can, however, convert it to any of the other curve types, e.g. to
133 change the type of arrowhead). The shape of the arrow will usually need
134 to be adjusted by shifting the control point that appears alongside it
135 in 'Move' mode.
136 Inserting text:
138 Text written into the text box can be positioned with the cursor and
140 may appear left, middle or right-aligned in the drawing. Text size and
141 color is selectable from a fixed list of choices. There are two spe‐
142 cial characters to be used for sub- and superscripting the following
143 character:
144 '^' to shift up (e.g. N^+)
146 '_' to shift down (e.g. CH_3)
148 The control character '|' is used to itializise the following charac‐
150 ter, as in |t-Bu.
151 A bold fonttype, typically used for numbering compounds, can be
153 selected by preceding the character with a '#'.
154 The special character '@' switches to symbol mode, which uses the stan‐
156 dard X11 symbol font. All alphabetic keys produce the corresponding
157 greek characters in this mode, and several other symbols are available
158 if their standard latin1 equivalents are already mapped onto the key‐
159 board:
160 yen -> infinity
162 hyphen -> uparrow
164 macron -> downarrow
166 The symbols 'plusminus' and 'registered' (trademark) are already in the
169 standard font, although they are not normally available on the key‐
170 board. Use the following commands (or add the declarations to your
171 .xmodmaprc ) to make them available via <AltGr>+<Key> (<Righ‐
172 tAlt>+<Key>):
173 xmodmap -e 'keysym r = r R registered' \
175 -e 'keysym o = o O yen' \
177 -e 'keysym p = p P plusminus' \
179 -e 'keysym u = u U hyphen' \
181 -e 'keysym d = d D macron'
183 (this leads to AltGr-P = plusminus, AltGr-R = registered in normal mode
185 and AltGr-O = infinity, AltGr-U = uparrow, AltGr-D = downarrow in sym‐
186 bol font).
187 For 'dots-and-crosses' diagrams, the following mappings to the symbol
190 font might be useful: acute -> cross (e.g. keysym x = x X acute) mid‐
191 dle dot -> filled dot (e.g. keysym d = d D periodcentered) (using the
192 degree sign for the open dot).
193 Circled versions of the plus and minus signs for denoting ionic charge
196 are available as @+ and @- .
197 When you want to use symbols as sub- or superscripts, place the sub- or
200 superscripting character before the '@' character, e.g. K_@a .
201 In text mode, the right mouse button deletes the label at the cursor
203 position. Changing the size, font or color of a label can be done by
204 left-clicking on it after choosing the desired combination of settings.
205 When the text entry box above the drawing area is empty, only the set‐
206 tings are updated without changing the contents of the label, otherwise
207 the label text is replaced as well. If you want to copy the text of an
208 existing label to the text entry box, click on it with the middle mouse
209 button.
210 Labeling shortcuts:
212 In all bond drawing modes, several keyboard shortcuts are available to
214 add atom symbols without having to leave drawing mode. The label is
215 placed at the current drawing position (the endpoint of the last line
216 drawn, or the spot last clicked on).
217 The keys 'c','h','n','o','s','p' and 'r' insert the corresponding capi‐
219 tal letter, 'l' (lowercase L) inserts 'Cl', while '1', '2', '3' insert
220 CH,CH_2 and CH_3, respectively. The asterisk key (*) inserts a filled
221 circle.
222 Pressing the space bar once allows you to enter arbitrary labels, which
224 will be placed at the current position when you press the Return key.
225 Drawing electron pairs
227 The keys of the numeric keypad can be used to draw short 'electron
229 pair' lines next to an element symbol - if one imagines the element
230 symbol to be sitting on the central '5' key, each key draws the appro‐
231 priate electron pair for its position. When used together with the
232 Shift key, two dots are drawn instead of a line - simply delete one of
233 the dots again if you need an odd number of electrons.
234 Numbering atoms
236 For quick numbering of the atoms in a molecule, switch to one of the
238 text modes, hold down the Control key and pick each atom in succession
239 with the left mouse button. Numbering starts at 1, and the sequence can
240 be reset at any time by clicking the right mouse button. If you need to
241 use your own numbering scheme, clicking the middle button (while still
242 holding down the Control key) makes it pick up whatever number is in
243 the text entry field.
244 Centering:
246 If there is not enough space for your molecule you can put it in the
248 middle of the sheet with the center button.
249 Exporting to foreign formats:
251 You can export your molecules as an X bitmap, a PNG or EMF image, an
253 encapsulated postscript file, an input file for Brian Smith' XFig pro‐
254 gram, an MDL ver. 2000 molfile for data exchange with commercial pack‐
255 ages, an SVG file for XHTML web pages, or in the PicTeX format for
256 direct inclusion in LaTeX documents. The PicTeX,PNG, EMF and Post‐
257 script output functions rely on the fig2dev program from the transfig
258 package and are only available when this program was detected on
259 startup. If the fig2sxd program is installed, an additional export
260 option is available for OpenOffice SXD format. Likewise, if the
261 (open)babel program is installed, an additional Export menu providing
262 access to all filetypes supported by this tool becomes available.
263 You can create the outputs in different sizes according to the current
265 zoom scale. Postscript and PicTeX files can also be created at arbi‐
266 trary scales selectable on the export file menu.
267 An option in the configuration menu can be set to call fig2dev in
269 international language mode, which will automatically render any text
270 written in the alternate (Times) font using the postscript font appro‐
271 priate for the current locale (currently Croatian, Cyrillic, Czech,
272 Hungarian, Japanese, Korean, Polish). See the fig2dev documentation
273 for details.
274 To include the PicTeX-file in your LaTeX document, you will need the
276 pictex macro package. Depending on the versions you use, you might also
277 have to load the 'color' package in the preamble of your LaTeX file.
278 If you experience 'TeX capacity exceeded' error messages, increase the
279 extra_mem_bot parameter in your texmf.cnf file (usually in
280 /usr/share/texmf/web2c, /usr/local/texmf or /etc/texmf). Pictex is
281 known for its unusual (by tex standards) memory requirements, and the
282 standard settings do not account for this (although you may find a com‐
283 ment a la 'change this if you use pictex' in the texmf.cnf file).
284 Something like extra_mem_bot=400000 should not hurt on any moderately
285 modern system.
286 Printing drawings:
288 Since version 1.5, direct printing of diagrams to a Postscript-capable
290 printing device (or more typically a print queue running ghostscript)
291 is possible. The paper size, magnification, printer name and the print
292 command to use (currently either lp, lpr or kprinter) can be stored in
293 the Configuration Dialog.
294 Selecting all or parts of a drawing for transformations:
296 Using the 'Mark' button, you can easily select parts of the current
298 drawing by enclosing them with a 'rubberband' rectangle.
299 If you need to add atoms outside of the rectangular area to your selec‐
301 tion, simply draw another rubberband around them while holding down the
302 Ctrl key.
303 The selected parts will appear highlighted in blue and are immediately
305 available for
306 moving:
309 simply drag the fragment to the desired position with the mouse
310 while holding down the left mouse button. (If you only need to
311 move individual atoms or bonds, you can simply pick and drag
312 them in 'Move' mode without having to mark them first).
313 rotating:
315 horizontal movement of the mouse translates to smooth rotation
316 around the pivot point selected when pressing the mouse button
317 flipping
319 (mirroring) the fragment about a horizontal or vertical mirror
320 plane through its center: this is performed by clicking on the
321 appropriate menu button
322 copying:
324 clicking on the 'Copy' menu button creates an exact copy of the
325 selected fragment slightly offset to the original. The mark is
326 automatically transfered to the new copy.
327 rescaling:
329 horizontal mouse movement is translated into a smooth increase
330 or decrease of size of the marked fragment
331 deleting:
333 to delete the marked fragment, simply click the third (usually
334 the right) mouse button after it is highlighted.
335 framing:
337 chosing one of the icons from the drop-down list of frame and
338 bracket styles draws the corresponding object, e.g. a pair of
339 round parentheses, around the highlighted fragment.
340 optimizing:
342 clicking on the 'bucket and broom' symbol invokes a function
343 that removes overlapping (duplicate) bonds and labels from the
344 drawing and straightens lines that are almost horizontal or ver‐
345 tical.
346 Adding previously saved figures:
349 To add another molecule from a previously saved chemtool drawing,
351 select it in the file selection window that comes up when you press the
352 'Add' button. Single clicking on any filename in the list displays a
353 small preview of the molecule to aid in selection. The newly added
354 molecule is automatically made active so that it can be repositioned as
355 desired.
356 If you want to add it to a predefined position on another molecule, you
358 can mark that attachment site by left-clicking on it instead of drag‐
359 ging the marker rectangle. A small green dot will appear at what is now
360 the reference position for the new part. If you save molecules with
361 such a marker set, it will in turn define their attachment site when
362 they are added to another drawing.
363 Adding one of the predefined templates:
365 Selecting 'Templates' from the 'Tools' menu opens a second window with
367 a small collection of predefined structures. Simply click on the image
368 of the desired molecule to add it to your drawing. The Template window
369 can be kept open throughout a chemtool session - if it is hidden by
370 another window, you can move it to the front by selecting the 'Tem‐
371 plate' menu in chemtool again.
372 The data in the template system differ from normal chemtool drawings
374 only by the fact that they are stored within the program, and in a
375 slightly awkward format (x and y coordinates listed separately in the
376 source file templates.h). These are meant to provide a convenient
377 basis set available to all users, but not individually extendable (you
378 can use the 'Add' function for your own structures). Please let us know
379 if you want specific molecules added to the templates - their name or
380 ideally a regular chemtool drawing file is all we need. (send email to
381 martin@ruby.chemie.uni-freiburg.de)
382 Importing foreign file formats:
384 Chemtool provides functions for importing files in both the PDB format
386 used by the Protein Database (and by most molecular modeling packages)
387 and the proprietary MDL molfile format used by ISISdraw and understood
388 by other structure drawing packages and database frontends.
389 As both are 3D file formats, while chemtool only handles 2D projec‐
391 tions, imported molecules are read into a temporary storage at first
392 and displayed in blue on the canvas. This 3D representation can then be
393 rotated using the mouse. Only after pressing the Return key on the key‐
394 board is it converted into the final 2D projection that can be edited.
395 While such a 3d import is in progress, all normal drawing and editing
396 functions are disabled.
397 With MDL molfile import, the carbon atom labels are automatically dis‐
399 carded. For PDB import, the amount of labeling can be chosen in the
400 file selection dialog, which offers retention of either all labels,
401 only those of non-hydrogen atoms, or only the non-numeric part of the
402 labels.
403 If the program babel is installed - either the original version written
405 by Pat Walters or the more recent OpenBabel effort - chemtool will
406 automatically offer a menu option for importing from any of the file
407 formats this supports.
408 Determining sum formula and molecular weight:
410 The distribution contains a helper program, cht, by Radek Liboska
412 (Prague) to calculate sum formula and (exact) molecular weight from a
413 chemtool drawing file. It is also available from within chemtool to
414 calculate these data for the current structure or a marked fragment of
415 it. Cht can be misled by duplicate bonds ( chemtool does not remove
416 overlapping bonds, such as they might result from fusing ring systems,
417 automatically) and by the 'aromatic ring' symbol, so you should avoid
418 these and check the plausibility of the generated sum formula where
419 possible.
420 Drawing functions not available within Chemtool:
423 For features not currently supported by chemtool, like general line-
425 drawing functions, getting Brian Smith's XFig drawing package xfig.org
426 is highly recommended. About the only thing it does not offer is sup‐
427 port for 'chemical' linetypes and drawing angles - which is why chem‐
428 tool was written as a sort of companion program. (There will probably
429 be more of the most sorely needed drawing options added to chemtool
430 over time, but duplicating the more general-purpose features of xfig
431 seems rather pointless.)
432
436 Chemtool and its companion program Cht are available under the terms of
437 the GNU General Public License (see the file 'COPYING' in the package).
438 This software comes with ABSOLUTELY NO WARRANTY.
439
442 Thomas Volk (original author and maintainer up to 1.1.1)
443 Dr. Martin Kroeker (maintainer and primary author since 1.1.2) mar‐
445 tin@ruby.chemie.uni-freiburg.de
446 Radek Liboska, PhD liboska@uochb.cas.cz
448 Michael Banck mbanck@gmx.net
450 and many others.
452 Webpage:
454 http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html
456
459 cht(1), xfig(1), transfig(1), babel(1), fig2sxd(1)
460 22 Jul 2007 Chemtool(1)