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 or add-in).
The presented drawing software applications work on the Windows or McIntosh platforms, some under Linux as well. 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 publication quality chemical drawing software applications on the MS Windows platform are reviewed and a few others are mentioned briefly:
Chem4Word, TouchMol for Office (add-ins for MS Office)
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. The distinction between and ranking of the lead applications is not so straightforward anymore: while in the first version of this review (1998) only three programs were included (ChemWindow, ChemBioDraw and Isis/Draw) and there were considerable differences between them, the drawing modules of the recent programs are side by side.
Although the official name is Accelrys Draw now, the program installs itself as Symyx Draw, as a member of the Isentris and Accelrys Direct information systems and Accelrys Electronic Laboratory Notebook. Accelrys Draw is the face-lifted new incarnation of the old ISIS/Draw with 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 Reaxys databases as well. Java applet version: JDRaw.
Chem(Bio)Draw is integrated with the Chem(Bio)Office, E-Notebook and other data management applications ("Ensemble for Chemistry"). The drawing of biological objects have been developed lately as well as integration with databases (with Scifinder recently). Available as Windows or Mac version. Version 13 has more bugs than its predecessors, version 14 is better. The ChemBioDraw for iPad is a considerably simplified version intended for basic molecular editing.2c,d,e
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. Available as Windows or as an older Linux version.
A new player in the field of chemical editors is ChemDoodle for Windows, Mac and Linux. It has everything necessary for creating publication quality chemical documents. It is integrated with ChemDoodle Web Components and ChemDoodle Mobile (iOS and Android phones). Its architecture is somewhat different from those of the old-timers, it has a handful of very useful brand new tools, a few new question-of-taste ones and some less impeccable features as well. In addition to structure and document editing features it contains several tools (some of them called "widgets") such as constitutional and physicochemical descriptors and properties, embedding, editing and simulation of spectra, etc. The main drawback of the previous versions that round-trip editing was a bit cumbersome in the Windows has been resolved.
SoftShell's old 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. The DrawIt modules of the ChemWindow and Academic editions are the same.
The latest version of Chemistry 4-D Draw contains 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). Available as Windows or Mac version.
Special mention must be made on MarvinSketch. This is an interesting and very dynamically developing Java-based multiplatform chemical editor for drawing structures, reactions and queries with excellent features for web applications. It is the input module of the JChem Base chemical information management system (and of many other ones such as Reaxys). Its general editing properties, support of other graphical objects and texts are not as polished and sophisticated as those in the above six applications – for the time being, it is not a publishing software, therefore no full comparison has been made. However, its chemical editing properties are very similar or even better in a few respects, especially the creation of query structures. The basic version contains several tools and plugins which are fully missing from the other applications or are available only by separately purchasing them. Although MarvinSketch is discussed only briefly and separately at the end of this review, it is referenced and compared at several points.
The different extensions (add-ins, plug-ins, bundled programs) come with the purchased versions, 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 review. The database and similar 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.
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 italizations point to 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.
The automatic installers of the programs support customised setup. As most of the programs comprise several optional modules, it is advisable to choose the custom setup mode and to select only the modules really necessary. All installation procedures were flawless except ChemBioOffice 13 Ultra: even selecting the custom setup mode, the appropriate dialog window was not initialised and the full package was installed (checked under Windows XP, Vista and 7/64 versions). This has been fixed in version 14.
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. 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 and most of them are 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 rule of thumb 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, ChemBioDraw suffers mostly from rare and unexpected crashes.
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, which include all objects of the drawing, and molecule files or molfiles, used mainly by modelling and database programs, these contain only the description of the molecules. Not regarding its own proprietary file formats (MDL SKC and MOL molfiles) Accelrys Draw has a narrow choice of export/import possibilities, mainly molecule and database file filters are available. Chemistry 4-D Draw accepts only MDL molfiles as well. MDL sketch files are supported by ChemBioDraw and ChemSketch, and vice versa, Accelrys Draw now supports the import of ChemBioDraw CDX files. ChemDoodle also supports the most important foreign sketch files. However, be prepared for inaccuracies during the import: fine tuning of the imported sketches is usually necessary. Of course, the not mutually supported features or objects will not be imported. DrawIt often crashed when tried to open ChemBioDraw files. MarvinSketch has the Document to Structure input mode: it supports the grabbing and opening of embedded structures from common Office document formats: DOC, DOCX, PPT, PPTX, XLS, XLS, ODT in addition to PDF, XML, HTML and TXT.
Support of Web-related file formats are also included in the latest versions (CML in ChemSketch and XML in ChemBioDraw and ChemDoodle, UniProt XML in Accelrys Draw); for the time being, these formats are in quite experimental phase yet and not of general use.
To summarize, ChemBioDraw and ChemSketch are the most respected applications followed by ChemDoodle and MarvinSketch, these applications contain the highest number of export/import filters (although in spite of intensive beta-testing not all of them are bug-free).
Support of own older file formats
During the evolution of these applications the structures of their own proprietary file formats evolved as well. Therefore backward-compatibility is never granted. For the time being, mentioned must be made on the following backward-compatibility issues:
DrawIt does not support the older CW2 format of its predecessor ChemWindow.
Accelrys Draw – As far as chemistry is concerned the backward-compatibility of ISIS/Draw created skc files is 100%. In the case of other graphical objects it is not fully compatible with its predecessor (most of the differences between ISIS Draw and Accelrys Draw are discussed in its Help). Some cosmetic and restyling should be necessary when using old files. The old TGF file format is not supported anymore. (Not too important, although it might be useful in special cases). Therefore don't delete the oldie but goldie ISIS Draw.
In ChemBioDraw 12 the handling of colours has been altered. Some surprises might happen in drawings using many colours (differently coloured shaded objects), or when pasting objects into other applications. For example, shaded or filled boxes behave differently. Other small inconsistencies have been found, too, for example arrows and font sizes of drawings created with earlier versions changed when opening in ChemBioDraw 12-14. Therefore make some tests before updating big projects, such as hundreds of figures for text books, just in case. Personally, I still use ChemBioDraw 11 when handling old projects.
No backward compatibility issues were experienced in the case of ChemSketch, 12-13 years old files of posters look flawless in the recent version.
Support of other graphical file types and embedded objects
This mainly concerns ChemBioDraw, ChemSketch and DrawIt as these applications are suitable for creating big size posters containing a collection of several data types. If illustrations, charts, diagrams are to be imported from another application, instead of bitmap images (JPG, TIF, GIF, etc.) vector formats (Windows metafiles WMF or EMF, SVG, PDF) should be preferred: the former ones cannot be resized without considerable loss of quality, so the printed images will look ragged, uneven. In some new versions the SVG vector format is also supported. The next table summarises the import possibilities of different files and clipboard objects into the programs:
As shown in the above table, MarvinSketch cannot import graphical images, however, with the aid of the third-party application OSRA chemical images can be converted to real chemical structures. OSRA (Optical Structure Recognition Application) is a handy utility designed to convert graphical representations of 2D chemical structures found in GIF, JPEG, PNG, TIFF, PDF, PS, etc. documents.12 The OSRA plug-in is available for Accelrys Draw 4 and ChemBioDraw 12, too.
Accelrys Draw, ChemBioDraw and ChemSketch have an Insert object option as well (direct calling of another Windows applications). Advanced users may experience with it, the results are mixed.
With the exception of DrawIt the programs have support for converting and saving the documents in other graphical bitmap formats. Avoid the use of JPG format as it is suitable only for photographic images. The lossless GIF or PNG file format can directly be used for creating web pages. (To learn more about the GIF, JPG and PNG formats read this side bar.) High resolution TIFF images are preferred by the traditional printing process. ChemDoodle supports several bitmap and vector graphical file formats, too. When the use of 2D vector graphics is advisable, SVG (Scalable Vector Graphics), an XML-based file format is an open standard nowadays for browsers and web applications.
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.
In ChemBioDraw 12-14 there are problems when saving the documents in some bitmap formats. When trying to save big multipage documents in PNG format, occassionally null files are produced. When saving in TIFF or PNG format, indexed colours are used (obsolete 256 colour mode), therefore the colours of shaded objects or the anatomy, animals, etc. templates are distorted. PNG files are unchangeably saved with transparent backgrounds, this can be problematic for unexperienced users.
Pasting of chemistry into other applications and back via the Window clipboard (dynamic object embedding)
Fortunately, there are no problems in the case of the most important task: the direct transfer of the drawings between these programs and other applications (text editors, Powerpoint, etc). The general object linking and embedding (OLE) 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 (round-trip editing).
Chemistry 4D Draw can accept sketches in MDL skc format from the clipboard, but only chemical objects (molecules) are supported.
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. Moreover, it is not possible to copy/past structures as chemical entities from DrawIt to any other chemical applications, the structures appear only as graphics. This is a serious drawback. You have to export them as mol files.
Accelrys Draw: Delocalized aromatic rings do not show, when they are copy/pasted into another application using the default paste operation. Use Paste as… or Paste special and select the Windows metafile (emf) option.
The latest versions of ChemDoodle already fully supports OLE procedures.
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 formats (wmf and emf), etc. On pasting the target program should recognise and use the appropriate ones. (Advanced users can fine-tune in ChemDoodle what is copied to the clipboard)
Although the chemical drawings embedded into a MS Word, WordPro or WordPerfect document can be re-opened and edited by their creator program later (round-trip editing), 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 make sure you 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 round-trip 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 and copy/paste it again from the drawing application.
An important feature is that ChemBioDraw, ChemDoodle, ChemSketch and DrawIt and are able to create multiple page documents or posters.
Preview and/or quick search
The Open file dialog of ChemDoodle, MarvinSketch and DrawIt contains a simple but extremely helpful quick preview pane. The preview pane in ChemDoodle contains even a magnifier, too. It displays a simplified version of the content of the current file. It greatly helps the location of a sketch or molecule, when a folder contains 200-300 of older files. The other programs should also consider the support of a similar feature.
Click on the images to open in bigger view:
Another helpful add-on of ChemSketch, ChemBioDraw and ChemDoodle is the quick search for structures feature. Contrary to ChemDoodle, this feature is not available in the basic versions of ChemBioDraw and ChemSketch, because it depends on the search engine of the corresponding database programs. In ChemSketch it enables the users to search for chemical structures on their file system in different chemical sketch and molfile formats as well as PDF, 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. 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 ChemBioDraw files. For the time being, it is somewhat slower and not so reliable as that one in ChemSketch, for example ChemFinder for Office 11 and 12 produced different hit lists from the same set of test files (using the same preferences). ChemDoodle searches in supported sketch and molecule files. The content of the matched files and structures can be inspected in the preview window and opened for editing.
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 six programs. In Chemistry 4-D Draw the moving of the different objects cannot be constrained to the horizontal or vertical direction. The next figure depicts the available different bond types. Some of them are query types as well, but can be used well in special circumstances. Mainly by Accelrys Draw, ChemBioDraw, ChemSketch and MarvinDraw 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.
Chemically interpreted multicenter (coordinative) bonds, such as the ferrocene molecule are available in ChemBioDraw, ChemSketch and Accelrys Draw. Of course, similar structures can be assembled manually from bits and pieces, when underlying chemistry is unimportant.
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, ChemBioDraw uses pseudoatoms for multicenter bonds, such as metal atoms coordinated to ferrocene. 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, ChemDoodle and MarvinSketch 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 (unfortunately, a later interconversion between the styles is not possible). Note also the very useful Lewis dot structures available in ChemDoodle:
All of the programs have a "Clean up 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. When applying it in ChemBioDraw 12-13, the algorythm often rotates flips even very simple structures, this is very unfriendly in our opinion. ChemBioDraw 14 behaves better
All of the programs can perceive aromaticity and replace optionally the double bonds with aromatic (delocalised) rings. Accelrys Draw cannot export aromatic rings via copy/past method into other applications, though.
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.
ChemDoodle contains several previously unknown or extended editing features, for example undo/redo with history window, automatic sizing of brackets to content, extended methods for centering or rearranging the objects, stack everything on page, saturate or "kekulize" molecule, graph reduction, etc. Some of these can be really useful while others belong to the question-of-taste category. ChemDoodle also contains tools for explicitly defining and building reactions in a separate dialog window. The reaction partners, reaction conditions, arrows and "+" signs are automaticaly assembled and formatted. (This tool is not for building reaction queries for database searches.) Its adventage is the quick and uniform formatation (consider the dozens or hundreds of reactions in a textbook), nevertheless, you have little control over the hard-wired layout (for example, automatic arrangement of vertical arrows is not fully supported.)
Line notations to 2D conversion:
Smiles, SLN or InChi strings (formulation of chemical structures in a line of text used mainly to facilitate the search in databases) are supported by ChemSketch, ChemBioDraw, Accelrys Draw, ChemDoodle and MarvinSketch. When you open a file of this type with a text editor you see something like this:
Strings do not contain coordinates, therefore while the conversion back to 2-dimensional representations of small molecules works well, in the case of large cyclic compounds the result will be chemically correct but quite ugly looking. The best results were obtained with ChemBioDraw when using Smiles strings while the others performed variously. For a not commented tiny comparison see this (There are several commercial and experimental applications out there to transform line notation of big molecules into acceptable 2D drawings.)
2D → 3D and 3D → 2D conversion of structures:
Delicate 3D structures should be imported from modelling programs. However, most of these applications have modules or bundled programs, add-ins, which are capable of 2D → 3D conversion:
Accelrys Draw: Convert 2D to 3D (add-in)
ChemBioDraw: must have Chem3D sister program installed
ChemSketch: 2D to 3D conversion included
Chemistry 4-D Draw: sister program ChemSite
DrawIt: bundled program 3DViewIt
ChemDoodle: NIH Cactus 3D builder (needs internet connection)
MarvinSketch: built-in 2D → 3D module or bundled program MarvinSpace
Except Chem3D all of these modules are free or come with the basic versions. 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 minimisations. 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 problematic. Nice drawings are usually produced only in the case of small molecules. A test was made using a 3D molecule file of josamycin, a macrolide antibiotic. Only the available options were used, sometimes repeatedly or in combinations. The results:
Accelrys Draw: clean-up of 3D files is not supported
Obviously the newest applications (MarvinSketch and ChemDoodle) did the best job. While ChemBioDraw could not produce satisfactory 2D structures from a bigger 3D molfile on its own, this is more successful if you have Chem3D, too. When the ChemBioDraw pane is active within Chem3D in dual link mode (the default case), edition or rotation of the 3D model is reflected simultaneously in the ChemBioDraw pane, the structure is on-the-fly converted to a 2D drawing. When the 2D model looks satisfactory, it can be saved or copied to the stand-alone ChemBioDraw program for further modification.
Biopolymer builder and interactive templates
This handy tool to produce peptides or nucleic acid sequences are included in Accelrys Draw, ChemBioDraw and ChemDoodle (without stereochemistry). The one found in ChemSketch is a quite immature version. The enhanced version of ChemBioDraw 13 and 14 supports the addition of β- and D-amino acids, disulfide bridges and the creation of cyclopeptides and arbitrary links between peptide chains. Protecting groups can also be added, but this function does not play well: the modified labels could not be expanded, even the example described in the manual could not be reproduced.
Click to open in full view
ChemDoodle has interactive templates for creating arbitrary carbon nanotubes and prisms. The width and height of the nanotube can be changed by moving the mouse horizontally or vertically. Double bonds will be automatically placed.
A new feature in ChemBioDraw, ChemSketch, Accelrys Draw, ChemDoodle and MarvinSketch is the optional drawing and/or export of sketches in anti-aliased mode: the elimination of the stair-step appearance of sloping or curved lines. This greatly improves the quality of drawings when exported to Powerpoint presentations or as images to web pages. Anti-aliasing has no influence on printing (the resolution of the printers is much higher than that of the screen). As it is a quite resource-demanding feature, in the case of slower, older computers and big multipage documents you may want to turn it off while the drawing is being prepared. The ChemBioDraw solution is the more advanced one: anti-aliasing is optionally used when pasting the drawings into other applications (Powerpoint, etc.) or saving as images or metafiles. ChemSketch uses only screen anti-aliasing (can be circumvented by use of a screen-capture application). The anti-aliasing in Accelrys Draw cannot be turned off – unfriendly solution because when moving sketches into other applications via the Windows clipboard, sometimes not all of the objects are anti-aliased.
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 ChemBioDraw and ChemSketch are the best: they contain more graphical objects than the other programs, on the other hand, these can be filled with simple or shaded colours and/or patterns. It is odd that pattern-filled objects are not supported in ChemBioDraw anymore. The support of Bezier curves (to create free-form, irregular curves or shapes) is the best in ChemSketch. Customizations of filling and colouring of different objects and their shadow are the most advanced in ChemSketch.
With ChemSketch a shaded double DNA helix can be created in five minutes. However, the new BioDraw templates of ChemBioDraw make the creation of DNA even more easier. Different basic atomic orbitals are available in all programs (although in different quality).
As mentioned earlier, in ChemBioDraw 12 the handling of colours was changed. This might cause problems in the back compatibility of drawings with many colors. The shadowed rectangles, etc. behave differently as well, and a white box with black shadow cannot be created even when trying to assemble it from two pieces.
The drawings of figure A were created with ChemBioDraw. The daunorubicin – DNA complex is from a Protein Data Bank file (PDB308D): the extracted structure was positioned with a 3D modelling program, transferred to ChemBioDraw as molecule file and some final touches were added. The middle sketch was produced with ChemSketch. A very powerful new feature of ChemBioDraw 10-13 is the BioDraw palettes and toolbar. Versions of ChemBioDraw with this new tool are called Chem & BioDraw. The BioDraw toolbar contains adjustable templates to draw enzymes, receptors, cell membranes, DNA, immunoglobulins, laboratory animals, etc. (figure B). BioArt templates have been added the latest ChemDoodle as well.
As for the rotations of different objects, ChemBioDraw and ChemDoodle are the most advanced: both chemical structures and caption texts can be freely rotated; 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. Accelrys 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 would be necessary, but 90° image rotation is not available in a less sophisticated text editor.
To summarize: ChemBioDraw and ChemSketch are about neck and neck. When creating complex drawings from the available graphical objects ChemSketch is perhaps a hair's breadth ahead. ChemBioDraw or especially ChemBioDraw has the adventage when assembling from templates.
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. ChemSketch, ChemBioDraw and ChemDoodle also contain templates for glassware (right image); additional templates are downloadable:
A very useful feature in ChemBioDraw and ChemDoodle is the TLC plate tool, especially for the users of laboratory e-notebooks. It allows the user to create and depict easily TLC plates 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 the former two it is quite clumsy (data has to be entered into a dialog table). A new gel electrophoresis tool has been added to ChemBioDraw 13.
Restyling of the sketches:
Another important feature is the possibility of the restyling of different drawing objects, for example the change of the appearance of arrows, the width of lines or bonds, margin width, font size and so on. Current settings can be saved from all programs and recall and apply later. Especially useful are the predefined journal settings (or style sheets). These are very flexible in the recent versions of all applications but in Chemistry 4-D Draw. In Chemistry 4-D Draw only the parameters of a full object can be modified, but not part of the object. In the other applications there might be some properties that can be set only globally, though, for example the display of aromatic delocalized circles in Accelrys Draw. The technical realisations are obviously different: for example in ChemSketch floating toolboxes are used, in ChemBioDraw right-click menus.
An inherited weak point in ChemBioDraw is the apply of style sheets and restyling of objects. No problems when creating a new document by opening a style sheet. However, when reapplying 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 always: odd font-size values might appear. Another bug in the latest versions of ChemBioDraw that on using the "Apply object settings from current document" option on imported structures, a clean-up procedure is also applied and this might mess up already nicely polished structures. Thirdly, if a structure is dowloaded and inserted into an existing document by using the "Find structure from name at ChemACX" way the document settings (bond length, bond width, etc.) are changed without warning! Could stuck as a great surprise later. Therefore it is highly recommended to put such structures into a temporal document first and then to copy it into its final place. Hopefully, these glitches will be fixed sometimes
Quite serious and very annoying bug in Accelrys Draw that when globally restyling an older document (e.g. changing bond width or turning aromatic circles on or off) positions of the objects are often messed up and all actual settings are re-applied (not only the changed one). In addition, this cannot be undone.