Isis ChemDraw DrawIt ChemSketch Chem 4D

Chemical Drawing Programs – The Comparison of ISIS/Draw, ChemDraw, DrawIt (ChemWindow), ACD/ChemSketch and Chemistry 4-D Draw7

Tamas E. Gunda

University of Debrecen, POB 36, H-4010 Debrecen, Hungary, e-mail: tgunda {AT} puma.unideb.hu

Last major update:16.05.2005

If you have any comment, do not hesitate to contact the author at the above adress.


Introduction
Setup
File operations, data movement
Drawing of chemistry
Other drawing operations
Text editing properties
Templates and group abbreviations
Chemical intelligence, nomenclature
Spectra and chromatograms
Other chemical adds
Drawing programs and the Web
Documentation
Summary
What else out there?
References, download
Summary of modules and bundled programs (Table 1.)
Tabular summary of comparisons (Table 2.)
On GIF and JPG…

Hungarian
Hungarian
version


Introduction

The immense development of microelectronics has banished the use of a typing machine, drawing pen, Indian ink and templates. Text editors like Word for Windows, WordPerfect or WordPro are of general use today. With the aid of these one can create professional looking articles and drawings, as well as a large amount of time for the rewriting, redrawing and making corrections can be spared. The creation of chemical structures with the conventional drawing software applications would be extremely painstaking and practically impossible. With publication in mind, aesthetics and quality come to the front, ensured by built-in templates, bonds constrained to fixed length and angles etc. 3D editing is usually not possible – 3D features of a molecule can be visualised only by using the wedged/hashed bond drawing methodology. The availability of different tools (palette of fonts, arrows, lines and curves, arcs and other shapes or graphic primitives, etc.) is also of high importance. If a true 3D representation of the molecule is needed, its import from a modelling program or 3D data base is the most feasible arrangement (although most recent drawing applications usually contain a simple 2D → 3D converter module).

The presented drawing software applications work on PC/Windows or McIntosh platforms. DOS programs are regarded to be obsolete today, however, it is necessary to mention that several 10-12 years old DOS programs are clearly better in a few respects compared with recent mammoth Windows applications with many bells-and-whistles. An important requirement is WYSIWYG (What You See Is What You Get). Under the Windows OS most tasks (printing, screen and printer fonts, resolution or any other system wide parameter) are maintained by Windows itself and its set-up is the determining factor. Another important point is the user-friendliness of the program. This means, that the interface moiety of the program, which ensures the interactive two-way communication between the user and the machine, should be simple but effective. The information sharing with other programs should also be many-sided.

In this article five of the most popular chemical drawing software applications on the MS Windows platform are reviewed:

ISIS/Draw 2.5 1 (MDL Information System) (updated June 2003)
ChemDraw 9.1 Ultra 2 (CambridgeSoft) (updated May 2005)
DrawIt - KnowItAll Academic Edition 4.1 3 (Bio-Rad) (updated May 2005)
ACD/ChemSketch 8.0 5 (Advanced Chemistry Development) (updated May 2005)
Chemistry 4-D Draw 6.0 Pro and 7.6 Lite 6 (ChemInnovation Software Inc.) (updated May 2005)
Mentioned briefly:

WinPLT, ChemPen, WinDrawChem, JChemPaint, MarvinSketch, JME Editor, BKChem

Although all of these software packages are stand-alone applications, they are members of integrated suites as well, they serve as the input modules of other database or modelling softwares: ISIS/Draw belongs to ISIS/Base, ChemDraw is integrated with ChemOffice, ChemSketch with ChemFolder, Chemistry 4-D Draw with Chem4D database. SoftShell's oldie but goldie ChemWindow has melted into the KnowItAll application suite and has been split to DrawIt and ReportIt – separate molecular editor and general editor applications, the latter is to import objects such as structures and spectra, arrange them on the page, and add text, annotations, reaction arrows, orbitals or other graphical objects (old ChemText users, remember!) – when I refer to DrawIt later, it implies always ReportIt, too. This ChemWindow → DrawIt transfusion is not without drawbacks, assets and bugs. The DrawIt modules of the ChemWindow and Academic editions are the same. Besides KnowItAll especially ChemSketch has several modules, extensions, and add-ins concerning the calculation of physical-chemical properties, import, processing and databasing of spectra and chromatograms, naming of molecules. prediction of NMR spectra etc. Several of the add-ins of ChemSketch can co-operate with other third-party programs such as ISIS/Draw and ChemDraw. In this latest upgrade only the Lite version of Chemistry 4-D Draw was tested; its drawing capacities and features are the same as those of the earlier 6.0 version. These extensions (add-ons, plug-ins, bundled programs) come with the purchased version, sometimes can be freely downloaded, sometimes must be purchased separately, sometimes are available as an Internet-service - therefore before making decisions it is highly recommended to visit the homepages of these programs and to inform, what modules are currently included in the price of the program & version being considered. These are briefly reviewed in Table 1. and near the end of this article. The database and other embedded functions of the programs are not considered in this review, but structure drawing capabilities and text functions have been probed in great details and aspects. WinPLT is differing so much from the other five programs, that it will be briefly discussed at the end of the review separately under the heading "What else out there".

As extended and detailed discussions of every features are not possible, the most important comparisons are summarised in Table 2. Bold text indicates features which have been considered clearly beneficial as compared to the other programs, while italization means weak points. Of course, we are aware of the subjectivity of such comparisons. On the other hand, only 10-20% of the users are advanced ones: those reading and studying the written or online documentation in detail, trying everything, and knowing such handy tools or tricks, which are unknown to the "everyday" user.

Installation



The automatic installer of the programs worked flawlessly in every case. As most of the programs comprise several optional modules, it is advisable to select the custom setup option, if available, and select only the modules really necessary. The installers usually provide some help in this phase, however, these are usually quite laconic - phrases such as "this option installs the ChemKingKong module" are pointless to a fresh user.

Generally speaking, programs which have specific input/output file formats usually use one or more specific file name extensions. These associations are always entered into the Windows registry. Most programs are able to deal with several other file formats too, like the graphical, image or text editing software packages, and the chemistry softwares we are dealing with fall also into this category. During the setup process some programs are quite aggressive and change the file name associations set previously by others. Fortunately none of the reviewed chemical softwares behave this way; ChemSketch is polite enough to ask in a dialog box how to handle the foreign file types (if the other program is also installed in your PC, don't allow to alter the corresponding association).

File operations, data movement

Beyond the basic file input and output operations, the export and import facilities to/from other applications are of high importance. For example, if one has to import a 3D structure from a modelling program or embed an illustration created by another drawing program.

* Support of foreign chemical file formats (filters)

There are two basic chemical file types: program-specific sketch files, these include all drawing objects, and molecule files or molfiles, used mainly by modelling softwares and they contain only the description of the molecules. From this respect the ISIS/Draw is the most conservative one, as it stubbornly handles only its own file formats (sketch files, molfiles, tgf files); in its latest version several chemical and graphical export formats have been added, but these are not available in the free version (the solution is weird indeed: instead of a warning dialog or greyed out options null files are produced; in order to convert you need the programs ConSystant and Chemeleon). Chemistry 4-D Draw accepts only MDL molfiles as well. The most common formats are ISIS sketch (skc or tgf), ChemDraw (cdx or the older chm), but be prepared for inaccuracies during the import, fine tuning of the imported sketch may prove necessary. Of course, the not mutually supported features or objects will not be imported. Bad news: DrawIt is not supporting the older cw2 format of its predecessor, ChemWindow, on the other hand, it often crashes when trying to open ChemDraw files. From this point of view ChemDraw and ChemSketch are the most respected, they contain the highest number of export/import filters (although in spite of intensive beta-testing not all of them are bug-free).

Support of Web-related file formats are also included in the latest versions (CML in ChemSketch and XML in ChemDraw); for the time being these formats are in quite experimental phase yet and not of general use.

* Support of other graphical file types

If illustrations are to be imported from another drawing application, instead of bitmap images the vector or metafile formats (WMF or EMF) should be preferred: the former ones cannot be resized without considerable loss of quality, the printed images will look ragged. The next illustration was used : the stylised cell was created with CorelDraw 8.0 and we tried to move and embed it into the five chemical drawing programs as WMF file, and next to move it together with the chemical structure into MS Word. Apart from Chemistry 4 D Draw, no problems were experienced.

fig. 1.


With the exception of ISIS/Draw and DrawIt the programs have support for converting and saving the drawing in other graphical bitmap formats. The GIF file format could be regarded to be the most important one as it can be directly used for creating web pages (by the way, a lot of graphical utilities are available on the web to convert a captured screen image to GIF or any other formats; for the GIF and JPG format see the side bar).

The general editor ReportIt supports a vast number of spectroscopical and chromatographical data formats, therefore it is surprising that it has no input/output options for WMF, EMF and at least a few common bitmap formats. Nevertheless, export/import via the clipboard was flawless.

* Pasting of chemistry into the text editor and back via the Window clipboard or dynamic object link

Fortunately there are no problems in the case of the most important task: the direct transfer of the drawings between these programs and other text editor applications. The general object linking and embedding procedure of the Windows applications is available: first time the drawing can be copied and pasted via the Windows clipboard or drag-and-dropped into the text editor. To edit later, double clicking on the drawing in the text editor (or using the right-click pop-up menu) starts the drawing program and moves the drawing into it automatically. The direct calling for the chemical drawing programs from another Windows application (or vice versa) is also possible (object insert).

Unfortunately, embedded ChemWindow drawings in older documents cannot be opened from the text editor and edited in DrawIt, in other words, the "ChemWindow object" does not exist anymore in Windows. However, you can copy the drawing and past into ReportIt (or any other application) as an image.

! Although the chemical drawings embedded into a MS Word, WordPro or WordPerfect document can be re-opened and edited by their creator program later, sometimes this procedure may fail: if the full document is interconverted (Word ↔ WordPerfect etc) or a newer version of the text editor refreshes an old document, the hidden link between the image and its creator program may mysteriously vanish. As a result, the image cannot be edited anymore. Therefore always save your (complicated) drawings from the chemical drawing program in its native format too!

! Windows 95/98/Me and Word specific: when opening a large document in Word, the program opens a great number of temporary files, among others one for each of the embedded drawings (or other objects). Therefore several dozens of files could be simultaneously opened. If the number of opened files is beyond a certain limit, Word may refuse to save the document and displays the Disk is full or too many files are open error message. To avoid this situation, enter the following line into the CONFIG.SYS file (or correct, if already present): FILES=96 (or even more). I have not come across this problem under Win2000/XP so far.

* Pasting of other drawings into the text editor and back via the Window clipboard or dynamic object link

To test this feature of the five programs the same drawing was used as above. First the image of the cell was copied from CorelDraw into the programs via the clipboard, then chemistry was added and everything together forwarded to Word. No problems arouse, apart from Chemistry 4-D Draw (unfortunately, it does not support the import of any graphics). The opposite way, i.e. moving chemistry into CorelDraw and then everything together into MS Word, worked flawlessly only in the case of ISIS/Draw and ChemDraw. Small discrepancies appeared in the chemical structure, when starting from the other programs, but this problem could be fixed:

! When pasting the above or any similar combined illustration into MS Word, and the result is not satisfactory, you may want to use the Past special… option of Word. Usually several suboptions appear (picture, enhanced metafile, different objects etc). Try these to achieve the best result. In the above example the metafile format proved the most satisfactory.

Generally speaking, the direct import via the Windows clipboard is a complicated procedure behind the stage. When a program sends a drawing to the clipboard, a mixture of different formats is used: the proprietary format(s) of the application, MDL's molfile (in text or clipboard format), sketch or reaction file, different picture formats, Windows metafile format may appear in the combination. Some of these formats are supported by the target program, others not, or are misunderstood. As a consequence, some experimentation may be necessary, but a common format can be found in any case. Tip...

An important feature is that ChemDraw, ChemSketch, DrawIt and Chemistry 4-D Draw are able to create multiple page documents or posters. Unfortunately, ChemDraw frequently crashes when using large multipage documents.

An useful add-on of ChemSketch is the document browser: quick previewing of existing documents without opening them. The other programs should also create a similar one, it would greatly help the location of a sketch, when your folder contains 200-300 of older ones. On the other hand, an extremely helpful new module in ChemSketch the Search for structure feature: it enables users to search for chemical structures on their file system in different formats including SK2, ISIS MOL, SDF, SKC, CHM, CDX, RXN, and PDF, as well as Word, Excel and Powerpoint documents and ACD databases, using exact or substructure search. The content of the matched files can be inspected in the preview window and opened in ChemSketch or in the application which created the file.. ChemFinder/Word is a similar utility capable of browsing MS Office documents with OLE objects and ISIS and ChemDraw files. Unfortunately, for the time being it is less advanced, slower and not bug-free. Quick search & preview of existing documents in ChemSketch

 

Drawing of chemistry

The basic operations, as for example the sprouting or free hand drawing of different bonds, the drawing and joining of rings, the resizing of elements or the whole picture etc, are handled well by all of the five programs. The only serious drawback of ISIS/Draw this respect that the moving of the different objects cannot be constrained to the horizontal or vertical direction, in Chemistry 4-D Draw it is cumbersome (entering of coordinates). ISIS/Draw supports only a minimum number of different bond types (not regarding the query bond types). The next figure depicts the available different bond types, not regarding normal 1-2-3 bonds. Some of them are quiery types as well, but can be used well in special circumstances. Mainly by ISIS/Draw, ChemDraw and ChemSketch several database features are supported: query atom and bond types, Markush bonds, chemically significant multicenter attachments to resonance delocalized fragments, polymers, reaction features, atom-atom mapping etc., these are not covered here. In ChemSketch there is a separate handy option button for the direct drawing of bonds with solid or dotted delocalization curves. Of course such structures, as simple drawings, can be assembled manually too.

fig. 2.


Another drawback of ISIS/Draw that all of the versions of this program have problems with the printing of dotted lines or bonds when using certain types of printers (we tried different HP LaserJet and DeskJet printers). A definite advantage of ISIS/Draw, DrawIt and ChemSketch over the others is that nearly every parameters of every objects of the drawing can be independently restyled and trimmed, a very useful feature in advanced hands. This was not possible in the previous versions of ChemDraw at all, but the latest versions already support this feature. In the case of Chemistry 4-D Draw the parameters of a full object can be modified, but not part of the object. When comparing atom properties, valence state, isotope mass, charge, among the five products Chemistry 4-D Draw is the weakest: it doesn't support charge as atom property but as a graphical object.

fig. 3.ChemSketch applies pseudo (empty) atoms for the bent bonds, like those used in carbohydrates. When converting to 3D structure, the program automatically eliminates these, but must take care when exporting such a structure into another application.

The basic default and user settings can be saved and recalled in all of the five programs, moreover, additional settings (styles) to produce documents according to the demands of a few common journals are also available. When three-dimensional structures are imported the recent versions of all programs are already capable of 3D rotation. Each program is able to the automatic addition of hydrogens, however, these are only implicit hydrogens, and the saved file will not contain them. ChemSketch has an option to convert and add implicit hydrogens as explicit, physical ones. This feature is the less sophisticated in DrawIt, for example no implicit hydrogens are added to imported molecule files, or corrected when editing later the bond order.

Chemistry 4-D Draw, when using its intelligent NamExpert feature, can create structures from chemical names in three styles: the generally used shorthand structure, the linear semistructural and the so-called Kekulé structure are the three available options:

fig. 4.


All of the programs have a "clean structure" function, which redraws and resizes selected structures or fragments to standardize all the bond lengths and angles. None of them has precedence over the others: they do their best and produce nice-looking structures, but may fail in more or less complicated ring systems.

* 2D → 3D conversion of structures:

Delicate 3D structures should be imported from modelling programs. However, these programs have modules or bundled programs, plug-ins, which are capable of 2D → 3D conversion:
Take into consideration that apart from Chem3D, these modules contain only simple MM optimisation algorithms, and the produced conformer is usable only for presentation purposes or as starting stage for more rigorous minimization. Using the peptide, carbohydrate and nucleic acid builder of the ChemSketch/ChemBasic Goodies, complicate 3D molecules can be created by inputting their shorthand text abbreviation.

 

* Full restyling of the sketches:

Current settings can be saved in the five programs and recall and apply later. Settings include such things as standard bond length, bond line width, margin width, font size and so on. Especially useful are the predefined journal settings (or style sheets). These worked in three programs as necessary, however, in ChemDraw, when applying a style sheet to an existing document or changing document settings not all of the new parameters are consequently applied. New documents will be drawn with the selected style, but this feature is a bit complicated when an existing drawing should be restyled according to for example JACS. In Chemistry 4-D Draw an existing drawing cannot be restyled in one step at all.

 

Other drawing operations



The drawing of different lines, polygons, circles and arcs, curves, arrows, etc. were also tested. Of course, no advanced features of a professional general drawing program should be expected, but basic functions are available, and these are usually enough to create, for example, simple diagrams or biochemical sketches. In this respect ISIS/Draw and ChemSketch are the best with ChemDraw only a little lagging behind: they contain a few more graphical objects, than the other two programs, on the other hand, these can be filled with colours and/or patterns.fig. 5. The treatment of opacity/transparency and layering of the different objects are the most advanced in ISIS/Draw and DrawIt. The editing of Bezier-curves (to create free-form, irregular curves or shapes) is the most advanced in ChemSketch. The simple or gradient filling of shapes with colours or patterns is best in this program as well – as a consequence, this is the only program, where a shaded double DNA helix can be created in five minutes.

The drawings A-E of the next figure were created with ISIS/Draw, although ChemSketch would have also been used. Their creation with the other applications would have been more difficult. However, drawing F was produced with ChemDraw, because the rotation of letters and texts in ISIS/Draw sketches (and Chemistry 4-D Draw) is not supported at all (in the case of this and all other drawings take into consideration that the screen resolution is far less satisfactory than that of a printer):

fig. 6.


The next sketch was created with ChemSketch:

fig. 6b.


As to the rotations of different objects, ChemDraw is the most advanced: both chemical structures and caption texts can be freely rotated, in the first case the rotation of the atom labels is an option.ChemWindow and ChemSketch rotate only the caption text, but not the structural text and atom symbols. ISIS/Draw and Chemistry 4-D Draw are not able to rotate caption text at all. The rotation of chemical structures and other objects could be important in the case of full-page figures: sometimes the use of the landscape mode is necessary, but it is not possible in all of the text editors, or the image cannot be rotated. (For example, in the older versions of MS Word it was possible to switch to landscape mode for a given page, however, the page numbering and the header was rotated as well, which was unacceptable in most cases. Therefore it was necessary to rotate the full figure counter clockwise prior to the insertion into the text editor.)

The drawing of laboratory glasswares or process flow diagrams is very handy in DrawIt: the library files contain a vast amount of drawings and chemical engineering symbols (the automatic snapping of glass joints together unfortunately has not been inherited from ChemWindow). ChemSketch and ChemDraw also contain templates for glassware (right image); additional templates are downloadable:

fig. 7. fig. 8. fig. 9.

TLC  plate tool in ChemDraw TLC  plate tool in ChemSketchA very useful brand new feature in ChemDraw is the TLC plate tool, especially for the fans of laboratory e-notebooks. It allows the user to easily create and depict a TLC plate with origin line, solvent front, and one or more lanes. The lanes can be populated with spots of different Rf, size, shape, or colour, and with option for automatic display of Rf values. A similar TLC tool is available in ChemSketch, too, as an installable extension, but compared to the direct graphical editing of its ChemDraw equivalent it is quite clumsy (data has to be entered into a dialog table).

Another important feature is the possibility of the restyling of different drawing objects, for example the change of the appearance of arrows, or the width of bonds and lines. ISIS/Draw, ChemSketch and now DrawIt are by far the most flexible in this respect, because practically every parameter can be changed for every object, one-by-one, grouped or for the whole drawing. In ChemSketch the parameters of a whole object can be tuned with the aid of floating toolboxes similarly to those used for example in the Corel programs. In Chemistry 4-D Draw the parameters of a full object can be modified, but not part of the object. Older versions of ChemDraw were the most inflexible: in several cases the object must be deleted and then to redraw. In the newest version this has been changed and several parameters of the individual elements can be set independently.

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