Chemdraw для mac os

ChemOffice and ChemDraw

This user guide helps you to activate, license and install ChemOffice or ChemDraw.

Hinweise

• The software is not free. You can order it from AcadCloud.
• If you have downloaded the software in a ZIP archive, unpack the files to your hard disk before the installation. To do so, copy the files in the ZIP archive to a folder on your hard disk or right-click the ZIP file and select Extract All .
• The license expires on the next 31 March . Afterwards, you have to obtain a new license.

Obtaining an activation code

1. Request your activation code
2. If you do not already have an account, register on this site with your u:account e-mail address. Log in after you have successfully registered.
3. Click OrderHistory on the left-hand side in the Software & Services section.

Now click the entry Site License Update DSK V17. (This entry can also have another, similar name.)

The activation code is specified in the column ActivationCode.

Installing ChemOffice on Windows

1. Download the file ChemOfficePro18.exe and/or ChemOfficePro18.exe from AcadCloud and open it.
2. Click Install Software .

Confirm the notification with OK.

Scroll to the end of the License Agreement, where you can accept it. To do so, select I accept the terms in this license agreement. Click Next.

Continue the installation by following the instructions of the installation software.

Next, open one of the applications in ChemOffice, for example ChemDraw. A window appears, prompting you to enter the following data:

• Name: Enter your name.
• Email: Enter your u:account e-mail address.
• Activation code: Enter your activation code.

Then click Activate to activate ChemOffice.

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ChemDraw Professional 16.0.1.4 – Chemists and biologists drawing tool

ChemDraw Professional is the complete drawing tool of choice for chemists and biologists to create publication-ready, scientifically intelligent drawings for use in ELNs, databases and publications and for querying chemical databases, now including SciFinder®.

• A single drawing solution that both chemists and biologists can trust to accurately handle and represent organic, organometallic and polymeric and biopolymer materials (including amino acids, peptides and DNA and RNA sequences) and to deal with advanced forms of stereochemistry.
• Chemists can use ChemDraw Professional to draw and submit chemical compound and reaction searches direct to SciFinder, with no more time-consuming cutting and pasting.
• Scientists can quickly, effectively and accurately communicate research and ideas using an extensive set of biological templates and drawing objects to create compelling illustrations of cells and pathways, including live chemical objects as needed.
• Scientists save time and increase data accuracy by using ChemDraw Professional to predict properties, generate spectra, construct correct IUPAC names, and calculate reaction stoichiometry.
• Find compounds (structures) of interest more quickly and accurately no matter the type of chemistry/type of structure. Better results from searches and less time spent searching creates more time for science.

ChemDraw is the world’s leading scientific drawing program. Hundreds of thousands of users benefit from its ease of use, high quality output, robust chemical intelligence, rich set of biological tools and integration in the ChemOffice Professional suite and with many third party products.

ChemDraw Professional includes the following applications:

• ChemDraw Professional is used by hundreds of thousands of scientists around the world to quickly and effectively draw molecules, reactions and biological entities and pathways for use in documents and electronic lab notebooks; to search databases, now including SciFinder; and to generate accurate names from structures and to predict properties and spectra.
• ChemDraw for Excel adds chemical intelligence to Excel spreadsheets so that chemists can use Excel’s analysis, sorting and organization tools to further manipulate and enrich sets of compounds and data and explore structure-activity relationships.
• ChemFinder Std is a chemically-intelligent personal database system that scientists use to organize their compounds and to search for and correlate structures with properties.
• ChemScript is scripting language that exposes the underlying chemical structure processing power of ChemOffice to developers who want to manipulate structures and automate processes.

• Release notes were unavailable when this listing was updated.

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Macs in Chemistry

Insanely great science

A Review of ChemDraw 17

ChemDraw is a very established chemical drawing package that probably sets the standard for publication quality chemical drawing. However, on the Mac platform in particular I think it is true to say Cambridgesoft have taken their eye off the ball and released versions that were not up to their usual standard.

ChemDraw 17 is in someways a fresh beginning, it is rewrite using a underlying codebase that is common to all platforms but then building on top of that to give a proper Mac look and feel (essentially porting the application over to the Cocoa development framework).

There now 4 different versions

ChemDraw Prime is the complete entry-level structure drawing program, with all the tools you need to quickly create chemically intelligent, publication-ready chemical structures and reactions, laboratory notes and experiment write-ups. Beyond a full set of chemical structure essentials (e.g. rings, bonds, chains, atoms and functional groups), ChemDraw Prime includes property calculators, chemical and lab equipment templates and handy TLC and Gel Electrophoresis Plate drawing tools.

ChemDraw Professional takes chemical drawing to the next level, with all the features in ChemDraw Prime plus: access to ChemDraw Cloud, biopolymer tools, BioDraw, NMR prediction, advanced Name to Structure, enhanced retrosynthesis tool, and even integration with chemical databases like including SciFinder®. ChemDraw Professional also enables structure data exploration supports organization and processing with ChemDraw for Excel, ChemFinder Standard, ChemScript and ChemDraw 3D.

ChemOffice Professional is the most robust, scientifically intelligent research productivity suite in the world. It builds on the foundations of ChemDraw Prime and Professional, and adds access to powerful tools like ChemDraw Cloud, ChemDraw E-Notebook, Chem3D and ChemFinder Ultra and 3rd party interacts — helping chemists and biologists alike efficiently keep track of their work, visualize and gain a deeper understanding of their results.

ChemDraw Direct modularized ChemDraw functionality for the web! Built on the latest in JavaScript and HTML5, ChemDraw Direct can be plugged into web browsers and internal applications that need to be chemicalized. Inside its lightweight packages, ChemDraw direct carries the core functionality of the ChemDraw family including: your favorite drawing capabilities, advanced Name to Structure, Structure to Name, Hotkeys/Shortcuts, Structure Templates and Structure Query Tools

As far as I can tell most of the extra tools in ChemOffice are mainly PC only, as are ChemFinder, ChemDraw for Excel, ChemDraw 3D and the interface to MOPAC, GAMMES etc.

Sadly the ability to script ChemDraw using Python is apparently Windows only which is a real shame. There is a comprehensive comparison available online

ChemDraw Direct is an interesting addition, it is presumably intended to replace the ChemDraw plugins and the mobile apps that were recently withdrawn. I hope to have a look at that later.

ChemDraw 17

Opening ChemDraw reveals a now familiar layout, it perhaps looks a little dated now but it has been honed over the years to afford a very efficient chemical drawing environment. However you will be delighted to know that it now supports high resolution displays

The first thing I noticed was that clicking on the «Help» brought up a blank Safari window, a check on the page source revealed a series of errors

It seems that Safari security is preventing display, I cut and pasted the URL into Google Chrome and the Help was displayed as expected.

Round trip Editing

Over the years this has been one of the features that has proved to be frequently broken during updates, i.e. the ability to copy and paste from a chemical drawing package into Word for example and then be able to copy and paste the structure back from Word into the chemical drawing application and then be able to edit the chemical structure. To give a little historical context

When copying a structure in ChemDraw 12.0.1 and below, the ChemDraw application would put a PICT of the image on the clipboard. We embedded chemical information into the PICT image, so that when that PICT image was transferred back into ChemDraw, the ChemDraw application would be able to interpret the picture as a chemically meaningful object that could be edited by ChemDraw. Due to continued modernizations in the Mac OS, newer applications are no longer supporting the PICT format on the clipboard. In newer applications, the use of PDFs to transfer copied images is now what is expected. This is why round trip editing between ChemDraw 12.0.1 and below and MS Office 2008 applications as well as iWorks applications ceased to work.

With every update to either MacOSX, ChemDraw or Microsoft Office there always the risk that something will break.

I’ve tested Office 365 (Word and Powerpoint) and I’m delighted to report that round-trip editing works as expected, similarly pasting into a FileMaker container field and then copy back into ChemDraw 17 works perfectly. Unfortunately pasting into Pages or Keynote results in the pasted object (PDF) losing all the associated chemical information and copying it back into ChemDraw only gives an image that can no longer be edited.

Support for HELM

Hierarchical Editing Language for Macromolecules (HELM) is a method of describing complex biological molecules. and first developed by Pfizer in 2008 DOI.

When biological macromolecules are used as therapeutic agents, it is often necessary to introduce non-natural chemical modifications to improve their pharmaceutical properties. The final products are complex structures where entities such as proteins, peptides, oligonucleotides, and small molecule drugs may be covalently linked to each other, or may include chemically modified biological moieties. An accurate in silico representation of these complex structures is essential, as it forms the basis for their electronic registration, storage, analysis, and visualization. The size of these molecules (henceforth referred to as “biomolecules”) often makes them too unwieldy and impractical to represent at the atomic level, while the presence of non-natural chemical modifications makes it impossible to represent them by sequence alone.

A more detailed description can be found here.

The various components are freely available on Github https://github.com/PistoiaHELM.

ChemDraw 17 Professional now features support for HELM notation and users can:

• Import, draw, edit and export complex biomolecular structures, containing natural or custom and unnatural monomers by selecting from a comprehensive list of peptides, nucleic acids or chemical protecting groups or via HELM strings.
• Paste a HELM text string into a fully chemically-interpreted HELM sequence that can be expanded and contracted as per your display needs.
• Easily search for specific monomers using the HELM toolbar filtering capabilities, through type-ahead filtering and, of course, structure search.
• Define and store your own custom monomers to be used into your HELM sequences.

If we take a HELM string,

In ChemDraw choose «Paste Special» and then «HELM»

The HELM string is pasted as a sequence.

We can check that this is a chemically aware sequence by right-clicking on one of the residues and selecting «Expand Label», this will reveal the entire amino acid side-chain.

You can do the reverse by selecting the structure and then choosing «Copy As:HELM». However you should note, don’t remove the residue label underneath the expanded structure, doing so will prevent you from returning from the expanded to the condensed representation and is also like to corrupt the «Copy As:HELM».

This all works because behind the scenes there is a database defining the monomers that are used, to see the monomers already defined choose » View>Show HELM Monomer Toolbar»

A: Polymer Type; B: Replace Current Monomer; C: Data source type; D: Open Monomer Editor; E: Spotlight search; F: Monomer Filter buttons

This panel provides a very efficient means to construct or edit large biomolecules, for amino acid and nucleic acids most of the monomer names are pretty obvious, however when you get to CHEM the short acronyms are not always obvious and it might be a nice addition to provide the option to display thumbnail image in a side panel similar to that used in the monomer editor.

It is also possible to create your own custom monomers by clicking on the «Open Monomer Editor».

To create a custom monomer:-

• Select the polymer type.
• Specify a unique Symbol and Full name for the monomer.
• Select a Natural analog and Monomer type (backbone /branch).
• Draw or paste the structure and select a label for collapsed state.
• Specify the label to be used when the capping group is in collapsed state.
• Click Save to Custom set.

However I assume that if you create custom monomers you will have to share your «database» together with any documents you have created that contain custom monomers, and of course there is always the risk that someone else will have used the same acronym? If you give someone a ChemDraw file it will transfer both the symbol and the underlying structure and should help resolve if there are conflicts, but this isn’t the case if you just transfer HELM strings on their own. HELM has the potential to be extremely useful but without a universal, curated database of monomers there is always the potential for errors creeping in.

The monomers are stored in json format which should help integration with other software.

Hotkeys

In ChemDraw 17.0, the way different hotkeys function have been modified to support much more efficient drawing, and some new hotkeys have been introduced to cover a wide range of possible organic functional groups. The modified hotkey functions are shown in the table below. All the previous atom labelling and bond hot keys seem to be still available, placing your mouse over an atom and pressing ‘F’ will change the atom type to Fluorine.

Function	Key(s)
Re-purposed to SPROUT “phenyl”	a
Re-purposed to GENERIC hotkey “Pen Tool”	l
Re-purposed to “O”	q
Re-purposed to GENERIC hotkey “Text Tool”	t
Re-purposed to GENERIC hotkey “Bracket Tool”	Shift+t
Re-purposed to SPROUT “methyl linear”	1
Re-purposed to SPROUT “carbonyl”	2
Re-purposed to SPROUT “phenyl”	3
Re-purposed to SPROUT “wedged bond”	4
Re-purposed to SPROUT “hashedwedged”	5
Re-purposed to SPROUT “cyclohexyl”	6
Re-purposed to SPROUT “methylidene”	8
Re-purposed to SPROUT “dimethyl”	9
Re-purposed to SPROUT “methyl cyclic”	0
Bond key: Re-purposed to FUSE RING “4”	4

A new copy/paste function has been introduced to aid reaction drawing. Simply select a molecule, then holding «COMMAND» and pressing arrows (right, left, up and down) will add an arrow and duplicate the selection on the other side of the arrow. A simple but very useful addition. To help with editing the Edit menu has additional items for handling text — Spelling, Substitutions, Transformations, Speech, Start Dictation and Emoji & Symbols

Document Properties

The document properties feature enables you to provide properties within a document which can be indexed by external aggregation engines like Attivio and Elastic search. However as far as I can tell these are not searchable by Spotlight and don’t appear in the «Get Info» window. You can simply add a variety of indexing terms as shown below. Note however that these are only supported in .cdx and .cdxml file formats.

Scripting

Once you have installed ChemDraw, a «ChemDraw» folder is created within your «Documents» folder this is where user defined monomers, templates etc. are stored. I noticed that there was also a «Scripts» folder.

If you place an AppleScript into this folder a new «Script» menu item appears on the top menu bar of ChemDraw.

This AppleScript takes the currently selected structure and searches for it in ChemSpider.

Since ChemDraw can also generate InChi keys you can also use this to search online databases for example this applescript https://www.macinchem.org/applescript/searchUnichem.php searches UniChem a new web resource provided by the EBI, it is a ‘Unified Chemical Identifier’ system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between databases. Currently UniChem indexes 33 online databases.

For example as the image below shows if you draw the structure of the NK1 antagonist Aprepitant, select it then run the script a web browser window opens containing direct links to the appropriate entry in a large number of online datasources.

Click image to expand.

In my limited testing, most old scripts will work fine, sometimes they need minor edits for changes to text in menu items.

Summary

This is a very welcome update to a popular piece of chemistry software, in my hands it seems that many of the bugs that dogged previous versions have now been resolved and that the new additions will be much appreciated. The addition of HELM notation support is welcome and the expanded Hotkeys should improve efficiency in structure editing.

Last Updated 9 October 2017

© 2019 Cambridge MedChem Consulting CC BY 3.0

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