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Chemical Drawing Programs – The Comparison of ISIS and Symyx Draw, ChemDraw, DrawIt (ChemWindow), ACD/ChemSketch and Chemistry 4-D Draw7
Introduction
The immense development of microelectronics has banished the use of a typing machine, drawing pen, Indian ink and templates. Instead, text editors like MS Word, Corel WordPerfect or Lotus WordPro are of general use today. With the aid of these one can create professional looking articles and drawings, and a large amount of time for the rewriting, redrawing and making corrections can be spared as well. 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. Direct 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 the recent drawing packages usually contain a simple 2D → 3D converter module).The presented drawing software applications work on PC/Windows or McIntosh platforms. DOS programs are not used anymore. 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 user interface 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 review the most popular chemical drawing software applications on the MS Windows platform are reviewed:
| ISIS/Draw 2.5 Free 1 | (MDL, now Symyx) | (updated June 2003) |
| Symyx Draw 3.2 Academic edition 1 | (Symyx) | (updated October 2009) |
| ChemDraw 12 Ultra, ChemBioDraw 2 | (CambridgeSoft) | (updated October 2009) |
| DrawIt - KnowItAll Academic Edition 4.1 3 | (Bio-Rad) | (updated May 2005) |
| ACD/ChemSketch 12.0 Free and Commercial 5 | (Advanced Chemistry Development) | (updated October 2009) |
| Chemistry 4-D Draw 8.3 Office 6 | (ChemInnovation Software) | (updated October 2009) |
MarvinSketch, WinPLT, ChemPen, WinDrawChem, JChemPaint, JME Editor, BKChem
Although all of these software packages are stand-alone applications, they are members of integrated suites as well, and they serve as the input modules of other database and modelling software applications or full information management systems.- ISIS/Draw and Symyx (formerly MDL) Draw belong to the MDL ISIS and the newer Isentris information systems. Symyx Draw is the face-lifted new incarnation of ISIS/Draw (in fact, rewritten from the skretch). It has a brand new and more user-friendly interface. A few new features – concerning mainly database use – have been added, a few drawing tools have been refined while a few other ones are not supported anymore. It is an alternative input modul to its own and the CrossFire database as well. Unless otherwise stated, referring to ISIS/Draw always implies Symyx Draw.
- Chem(Bio)Draw is integrated with the Chem(Bio)Office and E-Notebook. The drawing of biological objects have been developed lately.
- SoftShell's old and popular 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 – 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.
- ChemSketch is the input modul of ChemFolder and several other applications of the ACD suite. It 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.
- The latest versions of Chemistry 4-D Draw contain slight improvements over the previous ones. The commercial version of Chemistry 4-D Draw is integrated with its Chem4D database and nomenclature modules (depending on the purchased version).
- Of the other category, mention must be made on MarvinSketch. The newest and very dynamically developed multiplatform structure drawing package, with excellent features for web applications.
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, but these are usually quite laconic - phrases such as "this option installs the ChemKingKong module" are pointless to a fresh user. Every program has one or more specific, proprietary input/output file formats with unique 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 also fall 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 associations). A thumb of rule with every computer program that save your documents often! This is true in the case of the reviewed programs, too. Although they are generally stable enough, ChemDraw suffers mostly from rare and unexpected crashes. An interesting behaviour of previous ChemSketch versions that they didn't like the hibernation of the system. Version 12 does not exhibit this discomfort.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)
To summarize, 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 own older file formats
DrawIt does not support the older CW2 format of its predecessor ChemWindow.
Symyx Draw has sometimes problems when opening old ISIS/Draw sketch files (roundabout: open and re-save old sketch files with ISIS/Draw 2.5). As far as chemistry is concerned the backward-compatibility is 100%, but in the case of other graphical objects it is not fully compatible with its predecessor. Other surprises might also struck when trying to use files created by ISIS/Draw – don't delete this oldie but goldie version. The opposite is also true: ISIS/Draw crashed a few times when opening sketch files written by Symyx Draw.
In ChemDraw 12 the handling of colours has been altered. Some surprises might happen in drawings using many colours (several differently colored shaded objects), or when pasting colored objects into other applications.
Support of other graphical file types and embedded objects
Symyx Draw, ChemDraw and ChemSketch have an Insert object option as well. Advanced users may experience with it, the results are mixed.
With the exception of ISIS/Draw and DrawIt the programs have support for converting and saving the drawing in other graphical bitmap formats. The JPG format is suitable only for photographic images. The lossless GIF or PNG file format could be regarded to be the most important one as they 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; to learn about the GIF, JPG and PNG formats see the side bar). Although there is a Paste graphics option available in Chemistry 4D Draw, it did not work.
The general editor ReportIt supports a vast number of spectroscopic and chromatographic 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, the export/import via the clipboard was flawless.
Pasting of chemistry into other applications and back via the Window clipboard (dynamic object embedding)
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 and past the drawing 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!
When a sketch is pasted from any chemical applications to Powerpoint, a complex of data is inserted into it. This is usually unnecessary. Instead of using Paste, open Paste special... (if available) and select Picture (enhanced metafile). The amount of data is much less, and the Powerpoint file will be much smaller, especially in the case of many illustrations. Older laptops will be grateful.
The drawback of this method is that chemistry is not pasted together with the graphics, in other words, you can't edit the sketch in the original program anymore by simply double-clicking on it. So apply it only in the case of the final sketch, otherwise you have to delete it and copy it again from the drawing application
Generally speaking, 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.
An important feature is that ChemDraw, ChemSketch, DrawIt and Chemistry 4-D Draw are able to create multiple page documents or posters. Previous ChemDraw versions frequently crashed when using large multipage documents. This has been fixed in version 10.
Symyx Draw: Circles and delocalized aromatic rings look uneven, when copy/pasted into another application.
Quick search and preview
| An extremely helpful add-on of ChemSketch and ChemDraw is the quick search for structures feature: quick previewing of existing documents without opening them. Other programs should also create a similar one. It greatly helps the location of a sketch, when a folder contains 200-300 of older ones. In ChemSketch it enables the users to search for chemical structures on their file system in different formats including SK2, MDL 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. |
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| In the ChemOffice suite, ChemFinder for Office is a similar stand-alone utility capable of browsing MS Office documents with OLE objects and ISIS and ChemDraw files. The selected structures can be opened for editing or transferred into another document. For the time being, it is somewhat slower and not so reliable as the previous utility, for example ChemFinder for Office 11 and 12 produced different hit lists from the same set of test files (using the same preferences). These features are not available in the basic versions of ChemDraw and ChemSketch, because they depend on the search engine of the corresponding data base programs. | |
Hover the cursor over the images to get a bigger view.
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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 sketch etc, are handled well by all of the five programs. The only serious drawback of ISIS/Draw in 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. 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, advanced Markush structures, 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.
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Chemically interpreted multicenter (coordinative) bonds, such as the ferrocene molecule are available in ChemDraw, ChemSketch and Symyx Draw. Of course, similar structures can be assembled manually from bits and pieces, when underlying chemistry is unimportant.
A 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). This have been fixed in Symyx Draw. In all recent versions of these applications but Chemistry 4-D Draw nearly every parameter of every object and their elements can be independently restyled and trimmed, a very useful feature in advanced hands. In the case of Chemistry 4-D Draw the parameters of a full object can be modified, but not part of the object.
ChemSketch applies pseudo (empty) atoms for the bent bonds, like those used in carbohydrates. Similarly, ChemDraw uses pseudoatoms for multicenter bonds, such as metal atoms coordinated to ferrocen. When converting to 3D structures within the suit the programs automatically eliminate these, but must take care when exporting such structures to another applications.
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, although 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 the bond order later.
Chemistry 4-D Draw Pro, 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:
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.
The basic default and user settings can be saved and recalled in all programs, moreover, additional settings (styles) to produce documents according to the demands of a few common journals are also available.
Line notations to 2D conversion:
2D → 3D and 3D → 2D conversion of structures:
- ISIS/Draw: ACD/3D Viewer and 2D → 3D converter (add-in)
- Symyx Draw: Convert 2D to 3D (add-in)
- ChemDraw: sister program Chem3D (can be called directly as Chem3D Preview window)
- DrawIt: bundled program 3DViewIt
- ChemSketch: bundled 2D → 3D converter and ACD/3D Viewer
- Chemistry 4-D Draw: sister program ChemSite
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.
The automatic conversion of 3D structures to the usual 2D shorthand drawings using standard bond lengths and angles has always been always problematic. This is very easy if you have Cambridgesoft's Chem3D, too. When the ChemDraw panel is active within Chem3D in synchronized mode (the default case), edition or rotation of the 3D model is reflected immediately in the ChemDraw pane while the structure is on-the-fly converted to a 2D drawing (figure 5). When the 2D model looks satisfactory, it can be saved or copied to the stand-alone ChemDraw program.
Anti-aliasing:
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 ChemDraw and ChemSketch are the best: they contain more graphical objects than the other programs, on the other hand, these can be filled (simple or shaded) with colours and/or patterns. Isis/Draw has clearly lost its earlier leadership. Unfortunately, its successor Symyx Draw made even a backstep, smoothed curves and pattern-filled objects are not supported anymore. The editing of Bezier curves (to create free-form, irregular curves or shapes), customization of filling and colouring of different objects and their shadow are the most advanced in ChemSketch.
The drawings A-E of the left figure were created with ISIS/Draw, although ChemSketch or ChemDraw could have also been used. 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. Drawings like A, C and E cannot be prepared with Symyx Draw, because smoothed curves are not available. The middle sketch was created with ChemSketch. A very powerful new feature of ChemDraw 10-12 is the BioDraw palettes and toolbar. Versions of ChemDraw with this new tool are called Chem & BioDraw, the whole suite is ChemBioOffice. The BioDraw toolbar contains adjustable templates to draw enzymes, receptors, cell membranes, DNA, immunoglobulins, etc. (right figure)
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To summarize: ChemDraw and ChemSketch are about neck and neck. When creating complex drawings from the available graphical objects ChemSketch is a hair's breadth ahead. ChemDraw or especially ChemBioDraw has the adventage when assembling from templates.
As for 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.
The drawing of laboratory glassware 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:
| A 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). |
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Full restyling of the sketches:
In ChemDraw, when applying a style sheet to an existing document or changing document settings, not all of the new parameters are consequently applied. When drawings are copy/pasted between two documents with different settings, structural text is changed accordingly, but captions not. It's to be hoped that this glitch will be fixed in the next version of ChemDraw.
Quite serious bug in Symyx Draw 3.2 that when globally restyling a document with several objects (e.g. changing bond width) positions of the objects are often messed up.
editor. Optimized for the 
browser
Quick search & preview of existing documents in ChemSketch
Quick search of existing documents in ChemFinder for Office
Result of the quick search of existing documents in ChemFinder for Office
On-the-fly 3D → 2D conversion in Chem3D/ChemDraw. By rotating or editing the 3D structure in the left pane the changes are immediately reflected in the right pane.
