Macs in Chemistry

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ChemDraw Innovation Challenge

 

Perkin-Elmer have just announced the ChemDraw Innovation Challenge - a forum designed to shape the future of Chemdraw

For the past 30 years, ChemDraw has been known around globe as the premier chemical drawing tool for chemists and biologists alike. While each version has brought more powerful features (many of which came from feedback from our passionate user base), we’ve all had that moment where we wanted ChemDraw to do [X]. We want to hear your ideas, suggestions for new features, new third-party applications we should integrate and more. The sky's the limit - big or small, all ideas are welcome!


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ChemOffice and ChemDraw version 16.0.1 released

 

I just noticed that a new version of ChemDraw has been released.

ChemDraw and ChemOffice 16.0.1 provides a point release to address a number of usability concerns, primarily on Mac, identified subsequent to the 16.0 release. ChemOffice Pro, ChemDraw Pro, ChemDraw Prime and the ChemDraw Active-X control (CDAX) have been updated.

I have no details on what issues have been addressed, hopefully the topic on the Cambridgesoft forum will provide more user experience.

Forum Topic:- Update Chemdraw 16 Mac


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ChemDraw 16 Review

 

There is a review of ChemDraw 16 over on Chemistry and Computers.

A key feature is found-trip editing, wherein a user could make a drawing in one application, copy and paste the drawing into another application, and then later copy and paste back into the original application, and still be able to edit the drawing. Generations of Mac users relied on this feature to go from applications like ChemDraw into PowerPoint and back again. This has been has been regularly broken as we had various updates to Mac oSX, Microsoft Office, iWork and ChemDraw. It sounds like some interoperability has returned but it may depend on which versions of the various components you are running.

Now updated to include Mac OSX Sierra, ChemDraw 16 works and round-trip editing using Word 2011 still works! Unfortunately round-trip editing appears to be broken in Pages, Keynote and Numbers.


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ChemBioDraw and Word 15

 

A reader flagged this issue for me.

Word 2016 for Mac: I can't cut-and-paste an image from a vector drawing program I am a scientist and I routinely create images in a vector drawing program called ChemBioDraw. In past versions of Word, I was always able to copy these images to the clipboard and paste directly into the text of a document. With Word 2016 for Mac, all I get is many lines of gibberish code and no image. Am I missing something, or has the ability to handle vector graphics been eliminated from the program? FYI- a friend of mine who does design is having the same problem with a CAD program.

A quick search of the ChemBioDraw support forum highlights several threads that appear to be about the same issue.

I'm a new user of ChemDraw, and I have tried to copy/paste my structure into word and just end up with heaps of text like this:

0 0 0 0 0 0 0 0 0 0 0E 3.9121 2.7155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0E 3.9385 1.8909 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 0  1 3 4 0  3 4 4 0  4 5 4 0  6 7 1 0  7 8 2 0  8 9 1 0  9 10 2 0  10 11 1 0  6 11 2 0  12 13 1 0  13 14 2 0  14 15 1 0  15 16 2 0  16 17 1 0  12 17 2 0  2 18 1 0  18 5 1 1  19 20 4 0  19

With the rather unhelpful response

Currently our products are not supported with MS Office 2016. We plan to support MS Office 2016 for the future release/update.

The only thing I can suggest in the meantime is use the "Paste as PDF" functionality, this should allow display and round-trip editing.

I did a quick test with ChemDoodle and there don't seem to be any issues with this chemical drawing programme.


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Scripting Openbabel

 

@MatToddChem recently tweeted

Chemdraw file containing lots of molecules --> separate png/jpg images of each molecule. Anyone got a script that automates that? #headache

Whilst it is possible to convert a ChemDraw file to an image the problem is you get a single png file containing all the structures. In order to get individual image files it is first necessary to separate the individual structures. The easiest way to this is to convert from cdx to SMILES format. We can then take each of the individual SMILES strings and generate an image using OpenBabel all controlled by an Applescript.

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A first look at ChemBioDraw 14

 

ChemBioDraw 14 was released recently and I thought I’d download the demo version and have a quick look at it. I’ve written my first impressions here.


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Survey on ChemBioDraw

Perkin Elmer are looking for input on ChemBioDraw

Calling all chemists! PerkinElmer wants to know what changes you would like made to the #ChemDraw ChemOffice suite? What features are important to you? Which ones are needed? Which ones do you never use? Please help us design the future direction of this product by completing this short (1 page) survey

Given the comments I’ve received from readers this seems like a chance to at least get your views registered and ask for better Mac support.

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Export as mol file script updated

 

I’ve added a minor update to the Export as mol file script.

One of the issues with the original script that the mol file contains in its first line the incorrect title of the file (it appears to be the name of the document template).

When you just launched your ChemDraw application, or created a new document, the title would be “Untitled **”, such as "Untitled ACS Document 1996-1". When you save it as Mol file, its header block will inherit the current document title "Untitled ACS Document 1996-2”.

Untitled ACS Document 1996-2
ChemDraw12201318592D

14 16  0  0  0  0  0  0  0  0999 V2000

It would be better to have the molfile title the same as the file name the user enters in the dialog box, one way to achieve this is to “edit” the file and then save again to the same file name. We can do this by adding a line to clean up the structure and then saving.

try
save first document in (molAttachment) as "MDL Molfile”
--This is to ensure the title of the mol file is set correctly
do menu item "Clean Up Structure" of menu "Structure"
save first document in (molAttachment) as "MDL Molfile"
close first document saving no

If you now look at the mol file in a text editor you can see the title is set more appropriately.

Mol file1.mol
ChemDraw12201319082D

14 16  0  0  0  0  0  0  0  0999 V2000
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Export as mol file

 

A number of publishers are seeking to add extra value to publications by including access to chemical structure information to aid searching and indexing. More details are included in this comment from Elsevier.

Elsevier would like to enrich online articles by visualising and providing details of chemical structures you define as the main chemical compounds described in your article. For this purpose, mol files of the key compounds can be uploaded in EES. Please use your preferred drawing tool to export chemical structures as mol files and ensure that they are well defined and do not contain aromtic bonds, R-Groups or other variables. Submitted mol files will be available for downloading from your online article on ScienceDirect. Furthermore, Elsevier will generate InChI keys from the mol files and include them in the online article, which increase the online searchability of your article e.g. in Google. InChI keys will also be used to link the article to additional data in Reaxys.

Since you need to export each structure as an individual file this will become somewhat tedious, fortunately Brian Myers has written an applescript that greatly helps the process for ChemBioDraw users

Now updated.

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Applescript to search un1Chem

Un1Chem is 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 the uniChem contains data from 19 different databases:-

Since ChemBioDraw can generate InChi Keys I thought it might be interesting to write an applescript that access this service. The InChIKey is a short, fixed-length character signature based on a hash code of the InChI string. By definition, hashing is a one-way conversion procedure and the original structure cannot be restored from the InChiKey allowing confidential searching.

Full details are here



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ChemDraw for iPad

About three decades ago I stopped using a stencil and a Rotring pen to create chemical structures for publications and started using ChemDraw on a Mac, at the time it transformed the standard of structures in publications and it has continued to set the standard for publication quality chemical structures. Over the years the software has developed and moved into cheminformatics, spectroscopy and more recently biological drawing. This lead to the rebranding as ChemBioDraw but most of the chemists I know still call it “ChemDraw”. So it is perhaps not surprising that I feel rather pleased that the iPad version is entitled simply ChemDraw.

You can read a full review here.



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ChemDraw and Word compound numbering on Mac

A while back I got this question

”I’m about to hit the tedious part of writing my chemistry PhD thesis in Microsoft Word: having all mentioned compounds numbered in text and in the chemdraw imported files. My question: is there any automated option for this task or do I have to insert every number manually? In particular renumbering after adding a new compound in the middle of the text”

There are a couple of ways to do this in LaTex (http://www.jkwchui.com/2010/03/writing-chemistry-with-latex-33/) and (http://piti.exroot.org/konwerter/) but in my experience LaTex is not particularly popular among chemists. However help is at hand, I’ve just been sent details of a brilliant applescript that works with ChemBioDraw and Word.

The process is described in detail here (http://www.martinp23.com/blog/2013/03/chemdraw-and-word-compound-numbering-on-mac/) so I won’t give anymore details just to add that one thing I’ve been using in recent Chemdraw scripts is

tell application id "com.cambridgesoft.ChemDraw"

It avoids the problems with application naming with different versions of Chem(Bio)Draw Std/Pro/Ultra.

There are many more applescripts here.



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Copy file to Dropbox and email link

A while back I posted a script that copied a file to a users MobilMe Public folder and created an email link to that file. With the imminent demise of MobileMe a couple of people have asked me for a script that does the same but uses Dropbox.

This script shows how to copy a file to your Dropbox Public folder and then email a link to it.

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Script to email Chemical Structures

A reader commented that they often emailed ChemBioDraw .cdx structures to colleagues who it turned out did not have a copy of ChemBioDraw to view them, whilst it is possible to convert the cdx file to other formats using OpenBabel they usually just ended up exchanging an image. They asked if there was a better solution and this is an ideal task for Applescript. This script assumes the structure you want to email is open in ChemBioDraw, it will create an email using Apple Mail containing the structure as a SMILES string, and embed the .cdx file together with an image in PNG format.

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Scripting the Chemical Identifier Resolver

The name to structure feature in ChemBioDraw is very useful but is pretty much limited to systematic names and certainly does not support other chemical identifiers like CAS Numbers. There are a number of online services that do support these sort of functions but you end up having to cut and paste from different web sites. This is where the Chemical Identifier Resolver script comes into play.

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Scripting ChemBioDraw

A script to convert .cdx to .png file format Read More...
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ChemBioDraw 12.0.2

ChemBioDraw 12.0.2
CambridgeSoft have released an update for the Mac version of ChemBioDraw

Read More...
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Roundtrip editing

It looks like there is light at the end of the tunnel with regard to the issue of “round trip editing”. Read More...
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ChemBioDraw Roundtrip Editing

Yet more on the continuing saga of round trip editing using ChemBioDraw. Read More...
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ChemBioDraw Round Trip Ediiting

Workaround for ChemBioDraw roundtrip editing issues. Read More...
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eMolecules Applescript

Applescript to search eMolecules Read More...
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ChemDraw and dialog boxes

The upgrade to Mac OS X 10.6 (Snow Leopard) has caused a number of problems for ChemBioDraw (aka ChemDraw) users. One particular problem is the upgrade appears to have broken the ability to enter text into dialog boxes. Whilst this has been fixed in an update to version 12 of ChemBioDraw Cambridgesoft seem reluctant to provide an update for earlier versions of the software, suggesting instead that users should upgrade.

Unfortunately I don’t have ChemBiodraw 11 (or earlier versions) so I can’t explore the problem but perhaps it might be possible to offer a work around using Applescript.
Read More...
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ChemBioDraw Update

ChemBioDraw Update from CambridgeSoft. Read More...
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Please complain

A list of issues using ChemBioDraw 12 under Mac OS X, please use the link to the forum to register your concern. Read More...
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ChemBioDraw 12 Review

Review of ChemBioDraw 12. Read More...
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Tip for improving ChemBioDraw printing

I was sent this tip for improving the quality of printing from ChemBioDraw. Read More...
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Using HotKeys in ChemBioDraw

Tips and tricks for using hotKeys in ChemBioDraw Read More...
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ChemBioDraw Updated

ChemBioDraw has been updated to support Mac OS X 10.5. Read More...
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More ChemDraw issues

Problems with Word 2008 and ChemBioDraw. Read More...
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Applescript Tutorial 9

Embedding chemical metadata into image files. Read More...
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Applescript tutorial 8

Getting chemical structure embedded in images. Read More...
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Chemdraw Plugin

Issues with Chemdraw plugin. Read More...
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A Review of the latest version of ChemBioDraw

I've written a review of the latest version of ChemBioDraw (AKA ChemDraw) Read More...
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