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Chemtool(1)		    General Commands Manual		   Chemtool(1)

       Chemtool	Version	1.6.5

       chemtool	[<filename>]

       Chemtool	 is a program for drawing organic molecules and	exporting them
       as a X bitmap, PicTeX,  Xfig, SVG, MDL or EPS file. It runs under the X
       Window System using the GTK widget set.

       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.

       In  all	drawing	 and editing modes, mouse button one (usually the left
       button) is used to mark or draw objects,	while button three (the	 right
       button)	can  be	used to	delete objects of the current type. The	middle
       button is mainly	used in	the bond drawing modes where  it  allows  fast
       changing	 of bondtypes.	Starting with version 1.5, the default storage
       directory for datafiles,	and the	filename  extension  to	 use,  can  be
       saved via a configuration dialog.

       Drawing of bonds:

       Bonds  can  be drawn in 4 different angle settings (hexagon with	30deg.
       intervals, two pentagons	with 72deg. intervals (different orientation),
       and  a  45deg.  i octagon). (Intermediate angles	are possible in	all of
       these modes as well - just ignore the marker points in this case).

       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. (The
       color used for the bond is updated at  the  same	 time  if  necessary.)
       Pressing	 the  middle mousebutton on a bond when	in 'Bondtype' mode re-
       verses the direction of that bond.

       Using the third (usually	the right) mouse button	deletes	the bond  next
       to the cursor position.

       The available bond types	are :

       single bond

       double bond

       double bond (shorter line on the	other side)

       centered	double bond

       triple bond (flanking lines shorter than	central)

       triple bond (with equal line lengths)

       quadruple bond

       wedge-shaped bond

       dashed wedge-shaped bond

       wavy line

       half arrow

       regular arrow

       wide bond


       dotted line

       overlapping  single  bond  (which  cuts	out a segment from any bond it

       Semiaumomatic drawing of	rings:

       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	press-
       ing 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

       Drawing of curved lines:

       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	 func-
       tion,  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.

       Setting bond style:

       In  bond	 style	mode,  clicking	on any bond in the diagram changes its
       representation to the type selected in the pull-down menu next  to  the
       Type button.

       The additional bond type	available in the pulldown menu,

	      curved arrow

       is only available for drawing. It is actually a shortcut	for one	of the
       curve drawing functions described above,	with the second	and third con-
       trol  points  automatically generated. As such, it can not be converted
       to or from any of the conventional bond types.

       (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.

       Inserting text:

       Text  written  into  the	text box can be	positioned with	the cursor and
       may appear left,	middle or right-aligned	in the drawing.	Text size  and
       color  is  selectable from a fixed list of choices.  There are two spe-
       cial characters to be used for sub- and	superscripting	the  following

			'^' to shift up	    (e.g. N^+)

			'_' to shift down   (e.g. CH_3)

       The  control  character '|' is used to itializise the following charac-
       ter, as in |t-Bu.

       A bold fonttype,	typically used for numbering  compounds,  can  be  se-
       lected by preceding the character with a	'#'.

       The special character '@' switches to symbol mode, which	uses the stan-
       dard 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  key-

	      yen -> infinity

	      hyphen ->	uparrow

	      macron ->	downarrow

       The symbols 'plusminus' and 'registered'	(trademark) are	already	in the
       standard	font, although they are	not normally  available	 on  the  key-
       board.	Use  the  following  commands (or add the declarations to your
       .xmodmaprc  )  to  make	them  available	 via   <AltGr>+<Key>   (<Righ-

		       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'

       (this leads to AltGr-P =	plusminus, AltGr-R = registered	in normal mode
       and AltGr-O = infinity, AltGr-U = uparrow, AltGr-D = downarrow in  sym-
       bol font).

       For  'dots-and-crosses'	diagrams, the following	mappings to the	symbol
       font might be useful: acute -> cross  (e.g. keysym x = x	X acute)  mid-
       dle  dot	 -> filled dot (e.g. keysym d =	d D periodcentered) (using the
       degree sign for the open	dot).

       When you	want to	use symbols as sub- or superscripts, place the sub- or
       superscripting character	before the '@' character, e.g. K_@a .

       In  text	 mode,	the right mouse	button deletes the label at the	cursor
       position.  Changing the size, font or color of a	label can be  done  by
       left-clicking on	it after choosing the desired combination of settings.
       When the	text entry box above the drawing area is empty,	only the  set-
       tings are updated without changing the contents of the label, otherwise
       the label text is replaced as well. If you want to copy the text	of  an
       existing	label to the text entry	box, click on it with the middle mouse

       Labeling	shortcuts:

       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).

       The keys	'c','h','n','o','s','p'	and 'r'	insert the corresponding capi-
       tal letter, 'l' (lowercase L) inserts 'Cl', while '1', '2', '3'	insert
       CH,CH_2	and  CH_3, respectively. The asterisk key (*) inserts a	filled

       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.

       Drawing electron	pairs

       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	appro-
       priate electron pair for	its position.

       Numbering atoms

       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.


       If there	is not enough space for	your molecule you can put  it  in  the
       middle of the sheet with	the center button.

       Exporting to foreign formats:

       You  can	 export	 your  molecules as an X bitmap, an encapsulated post-
       script file, an input file for Brian Smith' XFig	program, an  MDL  ver.
       2000  molfile  for  data	exchange with commercial packages, an SVG file
       for XHTML web pages, or in the PicTeX format for	 direct	 inclusion  in
       LaTeX  documents.   The	PicTeX and Postscript output functions rely on
       the fig2dev program from	the transfig package.

       You can create the outputs in different sizes according to the  current
       zoom  scale.  Postscript	 and PicTeX files can also be created at arbi-
       trary scales selectable on the export file menu.

       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.
       If  you experience 'TeX capacity	exceeded' error	messages, increase the
       extra_mem_bot  parameter	  in   your   texmf.cnf	  file	 (usually   in
       /usr/share/texmf/web2c,	/usr/local/texmf  or  /etc/texmf).  Pictex  is
       known for its unusual (by tex standards)	memory requirements,  and  the
       standard	settings do not	account	for this (although you may find	a com-
       ment a la 'change this if you  use  pictex'  in	the  texmf.cnf	file).
       Something  like	extra_mem_bot=400000 should not	hurt on	any moderately
       modern system.

       Printing	drawings:

       Since version 1.5, direct printing of diagrams to a  Postscript-capable
       printing	 device	 (or more typically a print queue running ghostscript)
       is possible. The	paper size, magnification, printer name	and the	 print
       command	to  use	(currently either lp or	lpr) can be stored in the Con-
       figuration Dialog.

       Selecting all or	parts of a drawing for transformations:

       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	selec-
       tion, simply draw another rubberband around them	while holding down the
       Ctrl key.

       The  selected parts will	appear highlighted in blue and are immediately
       available for

	      simply drag the fragment to the desired position with the	 mouse
	      while  holding  down the left mouse button. (If you only need to
	      move individual atoms or bonds, you can  simply  pick  and  drag
	      them in 'Move' mode without having to mark them first).

	      horizontal  movement  of the mouse translates to smooth rotation
	      around the pivot point selected when pressing the	mouse button

	      (mirroring) the fragment about a horizontal or  vertical	mirror
	      plane  through  its center: this is performed by clicking	on the
	      appropriate menu button

	      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.

	      horizontal mouse movement	is translated into a  smooth  increase
	      or decrease of size of the marked	fragment

	      to  delete  the marked fragment, simply click the	third (usually
	      the right) mouse button after it is highlighted.

	      clicking on the 'bucket and broom'  symbol  invokes  a  function
	      that  removes  overlapping (duplicate) bonds and labels from the
	      drawing and straightens lines that are almost horizontal or ver-

       Adding previously saved figures:

       To  add	another	molecule from a	previously saved chemtool drawing, se-
       lect it in the file selection window that comes up when you  press  the
       'Add'  button.	Single clicking	on any filename	in the list displays a
       small preview of	the molecule to	aid in	selection.   The  newly	 added
       molecule	is automatically made active so	that it	can be repositioned as

       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 drag-
       ging 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.

       Adding one of the predefined templates:

       Selecting  'Templates' from the 'Tools' menu opens a second window with
       a small collection of predefined	structures. 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 an-
       other  window, you can move it to the front by selecting	the 'Template'
       menu in chemtool	again.

       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 ba-
       sis 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

       Importing foreign file formats:

       Chemtool	provides functions for importing files in both the PDB	format
       used  by	the Protein Database (and by most molecular modeling packages)
       and the proprietary MDL molfile format used by ISISdraw and  understood
       by other	structure drawing packages and database	frontends.

       As  both	 are  3D  file formats,	while chemtool only handles 2D projec-
       tions, imported molecules are read into a temporary  storage  at	 first
       and displayed in	blue on	the canvas. This 3D representation can then be
       rotated using the mouse.	Only after pressing the	Return key on the key-
       board  is it converted into the final 2D	projection that	can be edited.
       While such a 3d import is in progress, all normal drawing  and  editing
       functions are disabled.

       With  MDL molfile import, the carbon atom labels	are automatically dis-
       carded. For PDB import, the amount of labeling can  be  chosen  in  the
       file  selection	dialog,	 which	offers retention of either all labels,
       only those of non-hydrogen atoms, or only the non-numeric part  of  the

       If the program babel is installed - either the original version written
       by Pat Walters or the more recent OpenBabel effort -  chemtool will au-
       tomatically offer a menu	option for importing from any of the file for-
       mats this supports.

       Determining sum formula and molecular weight:

       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) and by the 'aromatic ring' symbol, so you	 should	 avoid
       these  and  check  the  plausibility of the generated sum formula where

       Drawing functions not available within Chemtool:

       For features not	currently supported by chemtool,  like	general	 line-
       drawing functions, getting Brian	Smith's	XFig drawing package from www-	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.)

       Chemtool	and its	companion program Cht are available under the terms of
       the GNU General Public License (see the file 'COPYING' in the package).
       This software comes with	ABSOLUTELY NO WARRANTY.

       Thomas Volk	(original author and maintainer	up to 1.1.1)

       Dr.  Martin  Kroeker  (maintainer and primary author  since 1.1.2) mar-

       Radek Liboska, PhD

       Michael Banck


       cht(1), xfig(1),	transfig(1)

				  30 Jan 2005			   Chemtool(1)


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