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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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November 26, 2012

Chemistry Software Questions Here

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Posted by Derek

As mentioned the other day, this will be a post for people to ask questions directly to Philip Skinner (SDBioBrit) of Perkin-Elmer/Cambridgesoft. He's doing technical support for ChemDraw, ChemDraw4Excel, E-Notebook, Inventory, Registration, Spotfire, Chem3D, etc., and will be monitoring the comments and posting there. Hope it helps some people out!

Note - he's out on the West Coast of the US, so allow the poor guy time to get up and get some coffee in him!

Comments (76) + TrackBacks (0) | Category: Chemical News | In Silico


COMMENTS

1. JB on November 26, 2012 9:40 AM writes...

Are there plans to improve the underlying architecture and UI of the ELN? I'm not a software engineer or DBA so I don't know if it something about the underlying database calls and/or front end, but both places I've worked over the last 9 years have used Cambridgesoft ELN and found it quite painful. Switching between folders and pages is sluggish, and there are all kinds of quirks about highlighting, copying, pasting, etc.

Permalink to Comment

2. BTDT on November 26, 2012 9:46 AM writes...

Mr. Skinner,  I purchased ChemDraw Ultra 12.0 on 9/15/10.  I am having major problems with embedded cdx files in MSoffice 2010 word and ppt.  I am using WIN7 64 bit.  When I open the embedded cdx file in CD, 7/10 times CD crashes and not only is the original embedded file messed up in ppt but sometimes other embedded cdx files in the same ppt file as well.  Is there an upgrade available to fix this?  If not, is version 13 more stable with my software/hardware platform?  Thanks so much for your help.

Permalink to Comment

3. Alain on November 26, 2012 9:49 AM writes...

Hi Philip,

This is more of a nuisance than a real problem, but no-one I've talked to so far has been able to help.

In ChemDraw, when you roll the mouse over an atom or bond, a filled blue box appears to indicate the current focus. This should (and usually does) disappear when the mouse moves away, but frequently it doesn't and the result can be frustrating, with a patchwork of blue boxes covering the molecule. Do you know what causes this behaviour, and is there any way to fix it?

For info, we are using ChemDraw Standard, version 12.0.2.1076, on Windows 7 (we saw the same behaviour under WinXP).

Many thanks,

Alain

Permalink to Comment

4. Chemjobber on November 26, 2012 9:50 AM writes...

What is the cost of a "legal" home copy of ChemDraw? (i.e. one for home use, for writing reviews and the like?)

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5. Charles Abrams on November 26, 2012 10:05 AM writes...

To what extent is it possible to control ChemDraw by scripting?

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6. Fred on November 26, 2012 10:12 AM writes...

I haven't see an OS X version of Chemdraw3D. Is there one?

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7. xyz on November 26, 2012 10:14 AM writes...

will you ever advertise and develop more basic user friendly hot key modifications, at least a basic hot key movement like marquee to bonding options (like the other day was shown here in a video clearly)?

this is the far most used mouse movement and it would helped a lot when drawing for presentations and so.

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8. skatesailor on November 26, 2012 10:16 AM writes...

As a retired organic chemist I no longer have an employer to provide a copy of ChemDraw, which I used for decades to prepare papers, patents, and reports. Now I correspond sporadically with a nephew teaching organic chemistry in Europe and doing research there. So, I could use a simple, affordable version of ChemDraw and would be willing to bear myself a one-time expense to buy it. But it must come with a perpetual license to control my costs, but with no upgrades save to accommodate new Apple operating systems. What can Cambridgesoft do for me?

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9. NH_chem on November 26, 2012 10:21 AM writes...

What would it cost for an individual owner to upgrade to the latest version?

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10. telomer on November 26, 2012 10:22 AM writes...

Before Chemdraw appeared in the market I used Chemwin for drawing structures which I no longer use. As a suggestion, it would be nice to add a menu with the most common commands used at the right click button in order to draw the molecule without the need to go all the way up to the toolbar or to the side to choose one from. It would be faster and very much like drawing on paper and this is one thing I miss from Chemwin.

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11. Javaslinger on November 26, 2012 10:26 AM writes...

Mr. Skinner,

My research group has been a long time user of Enotebook and certainly enjoy it's conveniences. What are the future plans for Enotebook and what improvements were incorporated into the recent release?

My main issue with program has been getting new users up and running. Each time we get a new researcher getting them connected seems to take an IT degree. Have improvements been made in that area?

Thanks

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12. PotStirrer on November 26, 2012 10:35 AM writes...

Dear Philip,

I have ChemDrawUltra 12.0.2.1076 and am using Microsoft Office 2010. When converting a Word file with embedded ChemDraw objects into a pdf document the images come out looking very bad. A colleague of yours a few months ago confirmed this compatability problem with Office 2010 (was not a problem with Office 2007). Do you have any idea when this will be remedied?

Thank you

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13. Young Padawan on November 26, 2012 10:41 AM writes...

I am, overall, usually satisfied with chemdraw, but there's two things I don't like at all.

1: I draw a lot of my TLCs in chemdraw. Usually I align it the way that the Rf value is nicely displayed next to a spot. If I however copy a spot using CTLR and drag and drop, the new spot gets labelled, too, however the label is not positioned next to the new spot, rather on top of the old label. This gets really annoying when drawing a lot of spots. Why is the relative positioning information not retained?

2. With one of the last updates the lines of the grid that you can switch of and on became really thick. Can I change this somehow? I like having a very thin grid around behind my drawings, for aligning purposes.But with the thick new grid, it gets really troublesome to see the structures, so I am not using this any more.

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14. PMP on November 26, 2012 10:45 AM writes...

It appears to me that ChemDraw handles fonts in a somewhat unstandard way. It is not uncommon, for example, that Greek symbols created with the Symbol font end up as unreadable characters when the artwork is copied/pasted to Word or Powerpoint. The only way to make sure that the graphical information is transferred without a glitch is to use .png format.

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15. chris on November 26, 2012 10:58 AM writes...

What is the Cambridgesoft strategy for supporting mobile devices. A substantial proportion of the people accessing my website do so using iOS or android devices. At the last review I did for a Pharma company 30 % of the committee were using iPads.

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16. Quintus on November 26, 2012 10:59 AM writes...

Some years ago CambridgeSoft abandoned Mac users and went hell for leather to the big industrial customers who all use Windows. Mac support is minimal, will this change? No.
The "chemically intelligent" Excel has never worked properly even on my windows machine. Will this change/work properly. No.
The support one gets as a user is miserable, will this change?No. Being now part of Perkin-Elmer will only make things worse.
In the meantime I've all but moved to ChemDoodle, which is cheaper and in many ways much better than ChemDraw.

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17. Philip Skinner on November 26, 2012 11:09 AM writes...

One correction - I don't work in support, so don't have the support answers at my fingertips. The best avenue for that is always the support website and posting a ticket there, so you can track the response. However I'll do my best at getting answer to support questions. My focus is much more on the 'how do I solve this problem with the tool' type. But all reasonable questions are welcome.

I'll get to 2-4 later. But for JB (@1), yes. The new UI is being released soon (v13.1). It has been updated with ribbon based menu's so it is consistent with the latest Microsoft style guides. It also allows users to switch on demand between the traditional tabular horizontal mode and a more "paper like" vertical mode. MS office objects can also be edited both inside the application, as before, and also externally in a launched Word etc. window.

The architecture has also been re-engineered, but the details of that would elude me bar that we have moved to .net.

I'm not sure about quirks of copying/pasting - in my prior life of using the ELN (up to v9 and for about 5 years) I never encountered any, neither have I since. I don't doubt you, just I can't comment. Wrt performance, the latest architecture should improve that somewhat. However the setup of the system has a much bigger effect - there is a tuning guide available for the server, and there are certainly ways to maintain your ELN to make it run faster (or slower) that have a much bigger effect that the underlying architecture.
There are certain other ways you can use the ELN that make certain tasks more speedy too - a big change has been in electronic signing. Post v1103 the traditional PDF rendering has become asynchronous, which means that it still takes the same time but you can do other tasks simultaneously now. The newer non PDF signing options are even faster, if your institution supports them.
Fundamentally every large system like an ELN would benefit from a periodical assessment of how it is used - matching up the way people use it and their workflows, vs the intended use, vs the functional capabilities of the existing system vs those available on newer systems.
That was probably more than you wanted, but I kind of got into my sweets pot a little here.

Permalink to Comment

18. Philip Skinner on November 26, 2012 11:09 AM writes...

One correction - I don't work in support, so don't have the support answers at my fingertips. The best avenue for that is always the support website and posting a ticket there, so you can track the response. However I'll do my best at getting answer to support questions. My focus is much more on the 'how do I solve this problem with the tool' type. But all reasonable questions are welcome.

I'll get to 2-4 later. But for JB (@1), yes. The new UI is being released soon (v13.1). It has been updated with ribbon based menu's so it is consistent with the latest Microsoft style guides. It also allows users to switch on demand between the traditional tabular horizontal mode and a more "paper like" vertical mode. MS office objects can also be edited both inside the application, as before, and also externally in a launched Word etc. window.

The architecture has also been re-engineered, but the details of that would elude me bar that we have moved to .net.

I'm not sure about quirks of copying/pasting - in my prior life of using the ELN (up to v9 and for about 5 years) I never encountered any, neither have I since. I don't doubt you, just I can't comment. Wrt performance, the latest architecture should improve that somewhat. However the setup of the system has a much bigger effect - there is a tuning guide available for the server, and there are certainly ways to maintain your ELN to make it run faster (or slower) that have a much bigger effect that the underlying architecture.
There are certain other ways you can use the ELN that make certain tasks more speedy too - a big change has been in electronic signing. Post v1103 the traditional PDF rendering has become asynchronous, which means that it still takes the same time but you can do other tasks simultaneously now. The newer non PDF signing options are even faster, if your institution supports them.
Fundamentally every large system like an ELN would benefit from a periodical assessment of how it is used - matching up the way people use it and their workflows, vs the intended use, vs the functional capabilities of the existing system vs those available on newer systems.
That was probably more than you wanted, but I kind of got into my sweets pot a little here.

Permalink to Comment

19. student on November 26, 2012 11:12 AM writes...

I agree with Quintus. Chemdraw has totally abandoned the mac user with the new version. Are they aware that Mac users make up the majority of academic chemists?

Do they know we can no longer copy and paste from chemdraw to word or other software from a mac?

Are they aware that chemdraw is the number one cause of instability on the macintosh, to the point of causing screen freezes and the like?

Are they aware that universities are seriously considering switching to Chemdoodle due to the aforementioned problems?

Permalink to Comment

20. Philip Skinner on November 26, 2012 11:13 AM writes...

Apologies all for not getting here sooner - between Pacific time, school runs and a tenacious flu things are moving slowly this morning. I see there are a few more things to catch up on, so I'll get cracking.......

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21. Philip Skinner on November 26, 2012 11:18 AM writes...

@7 Fred. There is no OSX nor has there ever been a Mac supported version, of Chem(Bio)3D. Your only option on a Mac is to use the PC version in parallels on something equivalent.

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22. Chris Swain on November 26, 2012 11:26 AM writes...

@21 Not quite true, prior to Mac OS X there was a version of Chem3D for the Mac, it never made the transition.

Permalink to Comment

23. Javaslinger on November 26, 2012 11:26 AM writes...

Enotebook and smart phones! Do you have plans to allow us to carry our Enotebook literally to the lab bench via some kind of Android app support?

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24. Chai on November 26, 2012 11:28 AM writes...

What are the job prospects like in the chemistry/informatics border area? What background do people usually have when they end up there? What does your day-to-day-job look like?

Background: I'm finishing up my PhD in organic chemistry, but I also love working with computers, programming, etc. I'm wondering if there are jobs that incorporate both.

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25. Philip Skinner on November 26, 2012 11:31 AM writes...

@5 Charles Abrams. There is a full API available so I believe that there is a very robust capability to add scripting. The devil is always in those details - but I would suggest that you get hold of the SDK and take it from there. To do that either contact your local sales rep or contact support - they should be able to get you the appropriate documentation. If you need additional help there is always the option to get service help from us.

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26. Philip Skinner on November 26, 2012 11:35 AM writes...

@23 Chris Swain - my apologies, I don't remember it but I guess we must have.

But no, no current plans that I am aware of for a Mac supported Chem3D. I will add it to our feature request list though.

Permalink to Comment

27. tocket on November 26, 2012 11:50 AM writes...

What is the easiest way to generate a Gaussian (or other quantum chemical software package) input file starting from a ChemDraw structure? Currently I use ChemDraw to draw the 2D structure, save it in the CML format, open it in Avogadro and perform a crude optimization before I can finally send it to Gaussian. The 2D->3D conversion that avogadro does from the CML file is rather poor though, so it takes considerable effort to shape the molecule the way I want. On the other hand Chem3D does a very good job if you just take a molecule from ChemDraw and paste it in. Unfortunately I can't save the Gaussian input file from Chem3D (Gaussian is run on a separate linux machine), which means that I still have to use avogadro.

Permalink to Comment

28. Philip Skinner on November 26, 2012 11:53 AM writes...

@23 Javaslinger

Nothing that I am at liberty to discuss right now. Actually, nothing that I even know, but that is intentional.

From a personal perspective though, I think that anything we do will probably focus on easy ways of getting specific types of data in, or out, that make sense for a mobile world. I love my smartphone but wouldn't think that it would be a very satisfactory place to prepare a full ELN record. But certain information would make sense to capture, or digest, in a mobile setting.

To date there have been a few incremental advances - namely......
1) a few industrial customers have explored using mobile access using either windows supported tablets, or via e.g. iPad using Citrix. Other options include desktop cloning tools such as iRemote or logmein. I've played with those myself, and still find the real estate to be too limiting to be really useful.
2) We did recently develop a web browser version of ChemDraw (for a collaboration with McGrawHill - we provide the embedded chemical drawing functionality for their online homework courses). Now, for them, it is a reduced version of chemdraw - they want their students to be responsible for drawing the right molecules and not rely on all the tools in chemdraw. But that version is to be available elsewhere.
3) We have been thinking a lot about the kind of searches people want to do of the ELN. The ELN is engineered to return experiments as search results (show me the experiment that contains..........) but as people add increasing amounts of structured property data (such as biological activity data), people want to ask property type questions (show me the compound that has property X and property Y). That is a logical search to do mobile, and is now straightforward using the Spotfire mobile app - *assuming the data is made available*. Traditionally that was actually pretty difficult and laborious, but some recent engineering changes in the ELN have made it much easier to get the structured data out to tools such as Spotfire for comparative analysis (such as SAR).

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29. Philip Skinner on November 26, 2012 12:02 PM writes...

@7 xyz

I must admit that I loved the video that Derek posted. I'd used ChemDraw since my undergraduate days, extensively through my doctorate, and throughout my career as a professional chemist. But I'd never thought to extend the hotkey set myself - I was happy if I could remember some basic keystroke shortcuts. But it is fascinating to see people run with the extensible capabilities.

I do think it is a great ideo to extend the provided set. I'll make sure that is added to our feature request list - all of these get reviewed by the development team.

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30. JB on November 26, 2012 12:08 PM writes...

@17- Thanks for the info- the copy/paste stuff I'm referring to is in things like tables or separate panes. Our system has been fairly heavily customized so there are a lot of tables and fields we have to fill out for experimental design- for example, reagent lists for buffers have a table where each column is an ingredient and each row is a property (name, vendor, part #, lot, etc.) You can only copy/paste one cell at a time, which means if you want to replicate part or all of the table on another page, you need to either flip back and forth dozens of times, or take a screen shot or print a hard copy and manually re-enter everything. Then, within those fields, things like line breaks or other unusual characters mess up the copy/paste as well.

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31. Joe The Chemist on November 26, 2012 12:08 PM writes...

I have been using ChemDraw for over a decade and never learned how to use it to its full advantage until Derek posted this video the other week: http://www.youtube.com/watch?v=03WNbvZLDkk

This is a much easier than reading the help files! Anyone who can get ten thousand people to watch a video about ChemDraw in a week is doing something right IMHO. You should seriously consider hiring this guy to produce your future instructional materials.

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32. Glenn Howes on November 26, 2012 12:10 PM writes...

As to problems with copy and paste on the Mac. The current version 13, should work much better than version 12 while used with modern versions of Office or iWork. I haven't seen a final copy of 13, or I'd say definitely. If you are using old versions of Office, then you are not going to have much success with copy and paste as the operating system has moved on. So, upgrade your old office 2008 copies.

ChemBioDraw 13 for Mac is capable of rendering absolutely beautiful PDFs and puts them on the clipboard. Older versions would put PICT clipboard flavors on the clipboard, and PICT just should not be used nowadays. When I was working for PE, I put a lot of sweat into getting the clipboard and printing working right, but I left several months before the final release.

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33. RB on November 26, 2012 12:48 PM writes...

The latest version of chemdraw available through our academic site license is ChemBioDraw 13.0. The Macintosh version of this program is unusable (crashes every 5 minutes or so, particularly if attempting to paste into a Word document – using OSX 10.8.2). The previous ChemDraw Ultra 12.0.3 was fine. As a Chemdraw user of over 20 years this is pretty disappointing to see, and am not sure what the future has in store – hopefully a revised version.

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34. Philip Skinner on November 26, 2012 12:48 PM writes...

@11 Javaslinger

How long do you have......... Improvement probably depend on what version you are on, but I'll try to give an overview.

The currently (or soon to be) released versions are 12.5 and 13.1. A few comments on those, and on features that came in in earlier versions too.

13.1 has the new GUI. It contains the structured data tool (Bioassay) and chemical synthesis. It has enhanced image handling, allows toggling between vertical and horizontal display modes, you can drag and drop sections to rearrange your order, has external word/excel/ppt editing, improved drag and drop of content into the notebook. It doesn't have Registration/Inventory integration currently, nor formulations, bioanalytical and R&D LIMS forms.

12.5 is the most recent notebook that contains all the modules (chemical synthesis, including registration and inventory integration, formulations, bioanalytical, R&D LIMS). It still has only the older GUI and only horizontal display mode.

As a round up of functionality that might be interesting that has come in in the last few versions....

1) a form for managing formulations/material science calculations
2) R&D LIMS for managing samples, requests and reports
3) asynchronous PDF rendering for archiving
4) In-system e-signing (without PDFs)
5) Bioanalytical specific workflows and forms
6) Incorporation of the structured data management tool (Bioassay) into the ELN architecture. This tool is good for bot biological assay information but also other tets and assays (particle sizes, rheology etc).

Specifically for your difficulties in adding users, is the challenge in creating their accounts, in setting up their user config folder, or in getting the client out to them? To respond to each......
1) Kind of depends if you are linked to LDAP. Adding users is normally a few clicks. Larger lists of users can be scripted in, which you may also do if LDAP linked. No real changes there recently, but I never thought adding users was challenging.
2) An older change was that if a user config folder was set up under a usergroup, a new user would automatically replicate that folder and it's contents upon their first login. In older versions you had to set that all up manually - laborious but not an IT professional skill.
3) Recent versions come with a Microsoft Click-Once installer which delivers the client (and updates) through a web URL. One click to install, along with the ChemDraw add-in if that is needed too. Any changes to the client are pushed autoamtically.

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35. Philip Skinner on November 26, 2012 12:56 PM writes...

@15 Chris

I'm not at liberty to discuss our full mobile strategy, not do I actually know it. As I responded earlier, I imagine it will concentrate on "sensible" applications - in that mobile devices are great for certain tasks and horrible for others. But that is pure conjecture on my part.

You mention your website though. I am going to assume that you run some kind of website where people can submit chemical type queries, through some kind of chemical structure drawing tool? An representative example might be an online database for methodology (Reaxys) or commercial availability (Sigma-Aldrich)?

Anyway, the one thing I can discuss is that we did just develop a javascript/HTML5 version of chemdraw. We did this for McGrawHill for their online homework courses - it became a bit cumbersome to have to install the embedded chemdraw plugin (active-x control) on everyones desktops. This tool can be available to other website developers on a case by case basis currently - I would suggest contacting your local sales rep if you want to investigate further.

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36. Philip Skinner on November 26, 2012 1:02 PM writes...

@7 Fred

The reason for the discontinuation of Mac support for Chem3D is that we enhanced the graphic rendering at some point in time, it is now on a platform no longer supported on Macs.

I'm not able to comment on future developments on this product, but we are certainly aware of the need for Mac and/or mobile support for this and other tools.

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37. Philip Skinner on November 26, 2012 1:08 PM writes...

Some general comments about Support. We do have a support team (which I am not in, but have been asking for help today with some of these questions). This kind of forum though is not a real substitute for using that resource for true support type questions. If you log your issue with our support team (http://www.cambridgesoft.com/support/) you can 1) access forums, tech notes etc. where ou can perhaps find someone who has had a similar issue resolved, and 2) track your ticket so you know what is happening on it at any time.

And I know it seems that it is crazy that we have allowed your particular issue to slip through, because everyone must be experiencing it. And sometimes they are. But more frequently we see issues that are really hard to replicate, that only occur for you (because you are that special). So, we will only resolve them if you tell us about them, and work with us to understand your environment.

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38. Philip Skinner on November 26, 2012 1:13 PM writes...

@2 BTDT

Yes, v13 is more stable. There are some known issues with v12 and Office 2010.

v13 also has some great new features so well worth upgrading - especially if you are under a site license where it is included anyway.

Office 2010 issues are probably best managed through our support team though (support.cambridgesoft.com) You may find this Technote useful:
http://www.cambridgesoft.com/services/DesktopSupport/KnowledgeBase/TechNotes/details/Default.aspx?TechNote=1124

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39. Philip Skinner on November 26, 2012 1:15 PM writes...

@3 Alain

I'm advised that this is probably an issue with your video driver. You should try updating that. If the problem persists, please contact support (support.cambridgesoft.com)

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40. Philip Skinner on November 26, 2012 1:29 PM writes...

@ 13 Young Padwan

re 1: That sounds like a bug, and one we haven't heard before so I don't have a resolution. Please can you log it with our support team (support.cambridgesoft.com)

re 2: sorry, you don't have an option to change the thickness of the gridlines. We did have a few comments that they had got thick/black on v12. They are thin and grey on v13 so moving to that version may be the best option.

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41. Philip Skinner on November 26, 2012 1:39 PM writes...

@4 Chemjobber, @8 Skatesailor

I don't have a SciStore pricelist handy - but am working on that. I don't ever actually sell so rarely deal with actual pricing. But, a few comments on pricing models.

We have 3 avenues for purchasing - through our online shop (SciStore), telesales and through your local sales rep. For individual copies, only the first two would really be relevant.

Chemdraw comes in 3 levels, standard, pro and ultra, with increasing capabilities across all three. It also comes in two licensing models - term (e.g. annual) and perpetual. You *can* choose to pay maintenance on perpetual licensing - most people don't, but why you might is that it keeps your support active, and also keeps you eligible for upgrades. Otherwise - you will reach a point where your software is not supported on the latest OS release on your Mac.

There are home and academic discounts. You are eligible for academic discounts if you are taking part time courses or have kids in school.

The institutional site licenses also often cover you installing on your home computer as long as your are still employed by your institution. So, for Milkshake this could be worth investigating. And for Skatesailor - you may be covered by your nephews academic sit license if your work is in connection with helping with his courses.

If this doesn't work for you, I would suggest you both try calling telesales. They might have more flexibility to work with you on some pricing, perhaps taking into account prior versions you've owned and doing it as an upgrade price or something. I can't speak for them, but you can certainly ask.

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42. Philip Skinner on November 26, 2012 1:44 PM writes...

@9 NIH_chem

That depends on what application you are referring to (I assume ChemDraw or ChemBioDraw), which level, when you bought your prior version etc. We do have upgrade pricing but it doesn't last for ever - you won't be eligible for an upgrade of your ChemDraw 6 to ChemDraw 13 for example.

You should check if your institution has a site license though - we do a lot with the NIH (where I assume you are) so you may be covered anyway. If so, your license may cover you for home use too.

Otherwise our telesales team would be the bet avenue to work with you - or just our online store. US telesales can be contacted on 1 800 315-7300 Online store at http://scistore.cambridgesoft.com/.

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43. Philip Skinner on November 26, 2012 1:52 PM writes...

General desktop (ChemDraw etc) compatibility notes are here and might be useful for some of the commentators:

http://www.cambridgesoft.com/services/DesktopSupport/KnowledgeBase/Compatibility/

The following also refers to copy/paste issues with ChemDraw and MS Office on the Mac:

Microsoft has released an update to Microsoft Office 2011 labeled 14.0.1 that now supports round trip editing of ChemDraw 12.0.2 structures.

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 iWork applications ceased to work.

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44. Philip Skinner on November 26, 2012 1:54 PM writes...

@14 PMP - I'm not sure I can help with this much. Fonts are controlled by your desktop environment, in your own system settings, and not by ChemDraw itself. If you have issues with fonts that you don't see in other applications I would suggest contacting support (support.cambridgesoft.com) who can work through this with you.

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45. Philip Skinner on November 26, 2012 2:00 PM writes...

@19 Student

Copy/paste from ChemDraw to Word on a Mac is fully supported. See my comment above (#43) as to why it wasn't for a period of time due to a change in the Mac OS and the way it handled embedded images. If it still doesn't for you you may need upgrades of Office or Chemdraw and I would encourage you to contact our support team to resolve your issue (support.cambridgesoft.com).

ChemDraw for Excel is also fully supported, any issues there should be reported but we haven't seen many.

We don't have any reports of instability on ChemDraw on MAc in our support queue - you really should report those if you see them. We can't help resolve them if we don't know about them.

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46. Philip Skinner on November 26, 2012 2:09 PM writes...

@42 Joe The Chemist

The video was great - I learnt a lot too.

Note we have started doing some of our own recently - there are a lot of tricks and tips that otherwise get hidden in the help files. These can be found here:

http://chembionews.cambridgesoft.com/media/featureclips/default.aspx?l=en

Note also that for institutions, there can be a lot of value in arranging chemdraw specific training sessions. We have a series of courses available, or can build custom content as needed.

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47. Philip Skinner on November 26, 2012 2:12 PM writes...

@42 was actually @32. Ooops.

@30 JB

The gaussian input file can be obtained by importing a molecule into chem3d, setting up the gaussian job and selecting the gaussian input format from the File->Save As menu

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48. Philip Skinner on November 26, 2012 2:14 PM writes...

Ooops again. #47 above was actually @27 Tocket.

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49. Philip Skinner on November 26, 2012 2:36 PM writes...

@30 JB
Thanks for the info. It's a little hard to comment without seeing your custom stuff. But I'll try to at least give some ideas......

It is correct that copying/pasting multiple fields from a table into another can be complex. Certain table types allow it, certain ones don't. One option could be to incorporate an export tool for the table - so you can export the table as an SD file, or CSV file or something similar, and then reimport into the new table.

It could be that your use-case would also benefit from some other functionality. I would encourage you to investigate the use of templates for example. Also, it sounded like you might be using the formulations/material science forms - those have in built screening tools that might also be relevant.

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50. Yulan on November 26, 2012 2:43 PM writes...

Are there any plans to make a Linux version? I've heard that running chemdraw in wine is less than optimal, and currently chemdraw is one of the only things keeping me in Windows, which I would rather not be using. Support for kbuntu/ubuntu would be appreciated.

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51. Betsy on November 26, 2012 2:44 PM writes...

My father is a retired organic chemistry professor, and is still working on getting those last few papers out for publication. Unfortunately, he had a stroke earlier this year, and is still having trouble writing by hand. He is not very computer literate, and has always written out structures by hand which my mom then recreates in ChemDraw. Since he can't currently draw structures (and Mom is not very chemistry literate), they're trying to come up with some workarounds to get his papers out. Ideally, there would be some sort of voice-activated software that would be able to draw structures based on his descriptions, but I'm guessing ChemDraw, etc do not have this type of support. Do you know of any voice-supported software that would do this? Alternatively, is there a way they could use ChemDraw differently to get around their "manually copying a written structure" strategy? Kind of an obscure question, I know. Thanks!

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52. Philip Skinner on November 26, 2012 2:56 PM writes...

@50 Yulan - Sorry, I am not aware of an current plans to make a Linux version of ChemDraw. I can add it to our feature request but I wouldn't expect there is a huge amount of demand for it.

As I had mentioned above a few times, we did develop an HTML5/web version which might be more broadly shared in the future. It is a lighter version of chemdraw, more of a replacement for the active-x plugin.

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53. takeachillpill on November 26, 2012 3:12 PM writes...

@19 Student

@45 Philip Skinner

Copy/paste from ChemDraw to Word is technically currently supported, but round trip editing (Word to ChemDraw) has a serious issue: loss of styles.

This is somewhat difficult to explain without confusion, but here's my try:

A ChemDraw has been created with custom style settings. It is pasted into word (or powerpoint) and the custom styled structures are still correct.

Now let's say a couple months down the line, you want to edit this figure in the word/powerpoint. If you copy and paste the figure into ChemDraw, it AUTOMATICALLY changes the style to the one currently active in ChemDraw. So if I have ACS 1996 style open in ChemDraw, I lose all customizations and the structures looks very strange.

Previous versions of ChemDraw would have a dialogue box like "The style of the objects is different from the document currently in use. Would you like to change the style?" This option is unfortunately no longer available.

This is a HUGE problem for many people, especially in my group where we need to revamp old presentations. Because of this issue, we often have to start over from scratch if we do not know what styles are used in the powerpoint.

I and many of my labmates (dozens over the years) have contacted ChemDraw support. Each time we are told a fix is in the works, but it have been over 2 years and no fix is available yet. We are then told that there is no way for us to get an update on when the issue will be fixed. This is rather frustrating as our research depends on this basic ChemDraw functionality.

ChemDraw support recommended use of Snow Leopard (OS X 10.6). However, this operating system has not be available on newly purchased macs since July 2011. Now OS X is on version 10.8. The recommendation of ChemDraw support to wipe the system and install a version of the operating system that is 2 years old is not a valid option for many people.

I know that you are trying your best, and we all appreciate all of your help. Please bring this issue up to support on our behalf. All our attempts to solve this simple problem have been unsuccessful up until now, and no solution has been reported.

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54. Philip Skinner on November 26, 2012 4:19 PM writes...

@51 Betsy

First, I'm sorry to hear about your fathers stroke. I hope he recovers more function soon.

There are a few things that *might* help but they might be more trouble than they are worth.

First, chemdraw (assuming that it is a high enough level) does have a capability where you can type a chemical name and it will convert it to the structure. So, if he can provide a name Chemdraw should be able to draw the structure. You could even use some voice recognition tool in windows to provide that input via voice. I caution however that my experience with voice recognition (thanks Siri) is pretty hit and miss.

Second, there are some tools out there that do optical structure recognition (OSR) on drawn structures to create chemdraw or other chemical structure files from them. Kind of like when you scan a document and it recognizes the text. However, these really only work best if the drawings are computer generated in the first place - they are really hit or miss on hand drawn images.

How many drawings are we talking about? If it isn't too excessive I'm sure that I, or other readers of this bog, might be willing to help out and take his hand drawn images and convert to chemdraw files. Derek can get you in touch with me.

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55. Philip Skinner on November 26, 2012 4:22 PM writes...

@33 RB

That is out of my knowledge area - I would suggest following up with support on that (support.cambridgesoft.com). I'll see what else I can find out wrt OS10.8 compatibility (see #53) but copy/paste is clearly an important functionality we would want to have working.

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56. Chemjobber on November 26, 2012 4:22 PM writes...

Philip -- thank you so much for the answer, and thanks for being willing to take on all the questions. Cheers, CJ

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57. Philip Skinner on November 26, 2012 4:36 PM writes...

@ 24 Chai.

An interesting question - and one perhaps relevant for the continuing discussions on alternate career paths for chemists that surface on this blog and others from time to time.

Perhaps a description of the roles in this industry would be useful. As perhaps people have been able to tell, just as is any industry, there are specialties - so, no I don't know everything there is to know about ChemDraw.

R&D/Engineering - drive the development of the product, including the design and coding

Product management - direct the planned future of the product including prioritising development, new features etc. Also create certain documentation and content.

Marketing/Field Marketing - a few roles including providing demonstrations, running pilots, attending tradeshows, creating presentations, talks, posters. MArketing communications focus mostly on creating collateral - web ads, print ads, brochures etc to get the word out on products.

Sales - split into field sales and telesales. ELN and other Enterprise systems can be very complex projects so boots on the ground are critical. Sales people aren't as bad as they are perceived by some - get to know yours as they can be a really useful resource sometimes.

Services - help deliver software - often the more complex systems that need more configuration to tailor them to the institutions unique environment.

Support - deal with questions for people who have bought the products, bug reports, feature requests, compatibility questions, some "how to" questions.

As I mentioned before, I am not in support, but actually in a field marketing role. My day to day job is a lot of going to potential customer sites and showing them how they would use the software. It tends to be more the Enterprise level software (Spotfire, ELN, Registration) than ChemDraw, although Chemdraw plays a part inside those other applications.

Getting into this industry is the same as any other really - timing, and perhaps knowing some useful people. Expect lower pay and worse work/life balance than an industry career - I can't comment on the stability but it can't be worse than drug discovery the last few years and is probably more transferable.

I'd be happy to respond to any additional specific questions, either here or if you contact Derek to put us in touch, then directly.

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58. Philip Skinner on November 26, 2012 4:38 PM writes...

@56 Chemjobber. You are welcome. I'm sorry I haven't got you an actual answer to your very specific question but I'll work on it more. I hope all the answers gave at least some value here.

I still haven't got that coffee from this morning, so perhaps time for a break....

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59. Rock on November 26, 2012 6:06 PM writes...

When pasting a SMILES string to structure in ChemBioDraw, the program always renders the aromatic rings with those ugly circles for the aromatic bonds. This requires quite a bit of reformatting before pasting in a presentation. Can this be an option to display as double bonds instead?

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60. Aswin on November 26, 2012 6:36 PM writes...

I also have the same problem as Rock .... Please clarify.....

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61. Aswin on November 26, 2012 6:36 PM writes...

I also have the same problem as Rock .... Please clarify.....

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62. Philip Skinner on November 26, 2012 6:50 PM writes...

@16 Quintus
I’m sorry you feel abandoned. It is true that most of the revenue, and hence most of the direction of the company, comes from industrial accounts which are dominated by PC use. But Mac support has always been important to us – some products have always made a lot of sense to continue supporting on the Mac (ChemDraw), some make much less sense to support (Registration) as they lie much more in the industrial realm anyway. However, we are increasingly moving to make our applications device agnostic where relevant.

ChemDraw for Excel (on Windows) works fine for me – and should do for you and everyone else. I have seen exceptions to that – but each was something wrong with the source file or messed up in a users environment – I’m not aware of any systematic issues currently. Have you registered your issues with support (support.cambridgesoft.com)?
I’m also sorry you feel that the support isn’t satisfactory and certainly would understand your reluctance to use it because of that. Have you tried it recently? The organization has tried hard to improve the support capability over the last few years – they can’t necessarily drop everything else to work on your bug right now but it has been redesigned to help you find out if a similar issue has been resolved for someone else, or if it is a known bug going through our bug fixing process, or where your particular bug is in consideration.

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63. Philip Skinner on November 26, 2012 6:54 PM writes...

@5 Charles Abrams
I noticed in ChemDraw v13 there is actually a menu item (file/chemscripts) and file/run chemscript that allow you to run python/chemscripts directly within the application. There may be some more description in the help files, or I can ask for more information if you like – although it looks pretty intuitive. The file/chemscripts allows you to store regularly used scripts (and share if appropriate). There are some preconfigured ones that come with the product anyway. The file/chemscripts allows you to run one saved in a directory somewhere.

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64. Philip Skinner on November 26, 2012 7:04 PM writes...

@59 Rock, @61 Aswin

The SMILES string describes if the double bonds in an aromatic should be depicted as localised or delocalised (as a circle). Upper case designate localised, lower case delocalised.

Thus for benzene, C1=CC=CC=C1 is the delocalised (kekule) and c1ccccc1 is the localised (circle) form.

Chemdraw respects the form that the SMILES string is in when drawing - but still understand the underlying structure and tautomerism.

ChemDraw 13 also respects the form a structure is in when copying as a SMILES string. I don't know if it did this on 12. Thus if it is drawn in delocalised form, the SMILES string copied will be of that form, similarly for the localised form.

I would suggest checking if you can change the output properties of wherever you are getting the SMILES string. Failing that you could either run the structures through a 'convert structure to name' and 'convert name to structure' loop or add a chemscript command to convert all delocalised aromatic to localised.

I hope that helped.

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65. bad wolf on November 26, 2012 10:14 PM writes...

Quintus, let's be honest: the 'academic market' means students who think everything in their computer is supposed to be free, and professors who don't want to pay for anything and are happy to turn a blind eye to a few surreptitious copies floating around the lab as long as they aren't on their grant. A business has to find business customers that can be held to contract if they want to stay in business (and develop, support customers, etc).

And sorry Yulan, that goes double for the Linux market, except add in the 99% of the population around the globe who don't want to pay for software.

Anyway, thanks to Mr Skinner for coming on here, and giving some interesting responses--such as that web-based service. I think that would be pretty popular with the infrequent user crowd!

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66. Charles Abrams on November 26, 2012 10:30 PM writes...

@63 Phillip Skinner - Thank you very much for the information. I haven't looked at the SDK and will start there. What I'm trying to do is pretty crazy anyway - I will contact you off-list.

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67. Charles Abrams on November 26, 2012 10:31 PM writes...

@63 Phillip Skinner - Thank you very much for the information. I haven't looked at the SDK and will start there.

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68. tocket on November 27, 2012 4:32 AM writes...

@47 Philip Skinner. Thanks for your reply! I hadn't noticed that you can save in the Gaussian input format before. I don't have any gaussian interface in my Chem3D though. I wonder if this is because I only have ChemDraw Ultra (with Chem3D Pro)?

Either way, being able to save the file as .gjf means I can open it in GaussView and quickly apply one of my predefined schemes. A definite time saver!

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69. M on November 27, 2012 8:18 AM writes...

Is there opportunity for the dynamic numbering of molecules that communicates with WORD(like the numbering of footnotes/endnotes in WORD)? A solution to this problem would be so helpful for writing reviews or theses.

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70. Javaslinger on November 27, 2012 8:59 AM writes...

Hi Phillip,

I guess I was not precise when I said the difficultly was with adding new users. That part is actually somewhat trivial. It's getting the new users 'connected' to the server that is a total crapshoot. We are using version the ChemBioOffice 12 suite so I don't know if that has that 'click once' feature, but it is difficult to navigate. All users work from the same campus but on their own PC's and there seems little reason why one can connect and another cannot.

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71. Glenn Howes on November 27, 2012 10:42 AM writes...

@takeachillpill which version of ChemDraw are you using, and which version of Office?

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72. Philip skinner on November 27, 2012 7:45 PM writes...

Sorry for not responding to the last few today - my day job has taken me away from the blog.

@M - an interesting idea. I'll pass it onto our product manager. I can certainly see the application, and we do have some tools that might be relevant for numbering reactants and products in a reaction.

@Javascript - I should qualify that all my responses re E-Notebook pertain to the Oracle Enterprise version. If you are using the desktop or SQL versions my answers would be different.

Regardless, it isn't clear to me if the issue is installing the client, or getting it to talk to the server. Assuming that there is a central server (ie not the desktop personal version) then any variance between the experience for different users is due to their PC environment - perhaps privacy or firewall settings. Past that - out of my league and best dealt with with a little consulting from our services team perhaps? If you do have the Oracle version then I would recommend using the click-once deployment - it really does make life easy.

Finally, for those that are interested - there has been a lot of discussion around ChemDraw v13. If you want to know what extra it does over v12, here is a little synopsis of the key functional improvements:

http://www.cambridgesoft.com/mobile/software/Version13Overview.aspx?cid=52

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73. takeachillpill on November 28, 2012 12:47 PM writes...

@Glenn Howes

ChemDraw 12.0.3.1216
Word 2011, Version 14.2.5 (121010)
OS X 10.8.2

All up to date with the most recent patches.

ChemDraw 13 is still not available with our academic license.

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74. Matt B. on November 29, 2012 11:58 AM writes...

Would it be possible to add a feature where compound numbering is synchronized automatically between a wordprocessing document and its embedded Chemdraw figures, similar to the way Word/Endnote tracks reference and figure numbers? I have wasted a lot of time renumbering compounds because someone wanted me to insert a figure near the beginning of a long document.

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75. Glenn Howes on November 30, 2012 11:37 AM writes...

@takeachillpill

Well, here I'm going to explain the problem, and believe me when I say this, I understand the problem as well as anyone on Earth.

There is a bug in ChemDraw 12 that causes it to crash sometimes when it gets a PDF on the clipboard from Office that ChemDraw didn't itself generate. This was my fault, and I apologize. Parsing other people's data is fraught with the dangers of assumptions. That bug should be fixed in 13.

ChemDraw 12 was a transitional release when it came to the clipboard. It placed a PICT on the clipboard, and if you checked the Add PDF to the Clipboard preference, it would also place a PDF. The 12.0.3 release would inject some ChemDraw specific info into the PDF so it could try to recover the chemical data if it ever got that back on the clipboard. In ChemDraw 13, the PICT generation was removed entirely, and now PDF (and a variety of chemistry specific formats) is placed on the clipboard. This PDF has a block of expanded metadata in compliance with the format supported by Apple with the OS X 10.7 SDK so that if you paste it into Word 2011 (I don't know the exact point release) and later copy and paste just that PDF back into ChemDraw you should recover an editable diagram. The version generated by 12.0.3 is a little incompatible due to a minor difference.

Word 2008 wouldn't work in this work flow because it would rerender the original PDF and thus throw away the ChemDraw metadata.

PICT had to be abandoned entirely as the operating system started automatically converting it to a TIFF on the clipboard, losing all the vectored, scalable flavor, along with the kicker of not honoring the PICT scaling, making every image 4 times as big on screen.

PDF is a wonderful format and much better than PICT in every way, but it didn't have a Apple approved location for application specific data until 10.7 so content creation apps (like Office or iWork) didn't preserve PDFs properly until that became publicized. Thus the reason PICT was supported for a couple years past its prime.

Amongst other things, PDF supports floating point coordinates, and Bezier paths, and PDFs embedded in Word documents will print beautifully, unlike the ugly low-rez results you will get on Intel based Macs with PICT embeds.

I highly recommend avoiding generating any more documents including PICT based ChemDraw clipboards, just in terms of long term data usability. At least with ChemDraw 13, you are dealing with a PDF (ISO 32000), with a compressed CDXML chunk of metadata (CDXML is publicly defined), as opposed to the old days of the chemical data being stored in a proprietary PICT format which is now dead, as individual PicComment blobs. If worse came to worse, the new clipboard could be reconstituted from their respective specs.

So, I would advise getting a demo version of ChemDraw 13 and checking it out. If not, you could try checking that "Add PDF to the Clipboard" setting if you haven't already.

Disclaimer, I no longer work for PerkinElmer/Cambridgesoft. I can only hope that this information is still up to date.

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76. BioBritSD on January 21, 2013 5:30 PM writes...

@takeachillpill and re ChemDraw 13 is still not available with our academic license

Not sure if you will se this, so long after the fact, however.......

That depends on your license. If your academic (or any other) institution buys individual boxes (i.e licenses) of chemdraw, you'd need to buy a new box (i.e license) to get the new version.

However, if they have a site license, or purchase individual term licenses, then you are automatically eligible for the latest version as soon as it comes out. Your internal administrator may however either not have bothered telling you, or may actively have a reason for you not to upgrade. Either of which is outside of our control, as far as we are concerned you can upgrade.

Full licenses are like a purchase, term licenses are like a lease. Site licenses are always term licenses.

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