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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.

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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.

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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.

Permalink to Comment

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.

Permalink to Comment

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.