editing Marvin pictures in MS Word

After I paste a ChemDraw picture into an MS Word document, I can later copy the picture, paste it back into ChemDraw, and edit it. I can't seem to do the same with a Marvin picture that I paste into a Word document. This is a serious limitation when I am writing a paper or a book, because it means that I need to save a separate Marvin document for every picture in my paper, rather than just copying the ones I need to edit as I need to edit them. Is it possible to devise a way to paste the Marvin picture back into Marvin so I can edit it?

I can hardly believe that an "editable image" would have been pasted into ChemDraw.


Probably, ChemDraw pastes an OLE object into Word. If it is OLE, it is editable (directly) in the MS-Office document.


(By double clicking on the "pasted image" in Word, the proper editor should be opened.) When you copy it back to ChemDraw, also an OLE will be pasted into the hosted application (ChemDraw). ChemDraw may retrieve the chemical structure from the pasted ChemDraw type OLE object.


Marvin also supports OLE, so you can do the same thing with Marvin (copy to Word, and copy it back to Marvin).


This feature will be available in the Marvin 4.2 release. You can already try it in the latest alpha release of 4.2. It is still under testing. After then, we also add this feature to the current Marvin branch (4.1.x). Thus, OLE support may be available earlier in fix releases (before the official release of Marvin 4.2).

I don't know what from ChemDraw is pasted into Word, but the picture is not editable as a ChemDraw document within Word. (If you try to edit the picture in Word, you are warned that you will lose vector information in the image.) To edit the picture as a ChemDraw document, you need to copy it and paste it back into Word. Whatever information in the picture allows ChemDraw to recognize its components is preserved when the picture is pasted into Word and then carried back into ChemDraw when the picture is pasted back into ChemDraw.





Anyway, I'm glad to hear we will be able to copy and paste back and forth between Word and Marvin 4.2 in the near future. I will download the latest MarvinBeans 4.2 prerelease and play with it.

I forget to mention that OLE supports requires a Windows operating system. As I remember, you use OS X. Actually, on which platform did you test ChemDraw?

I'm using MacOS 10.3 and 10.4, of course. And I've been using ChemDraw for over 20 years, so I know how it works. It has worked this way for as long as I can remember on both PCs and Macs. It has always preserved the ChemDraw information in the Word picture so that when you copy it and paste it back into ChemDraw, you can edit it again.





Back in the mid-90's, there was a time, Word 5 and ChemDraw 3, when the two programs worked together even more beautifully. You could merely double-click on a ChemDraw picture in Word, and a ChemDraw editor window would pop up with the picture. You could then edit it, and when you closed the window, your changes would be incorporated into the Word document. There was no need to copy and paste, except for the first time you put the ChemDraw picture into the Word document. But then Microsoft decided to change the way it handled graphics, and the behavior has never been duplicated since.

Hi Bob,


Thanks for sharing experience about ChemDraw - MS-Word copy.


In first view, I thought that you talked about Windows OLE copy. OLE has got this behaviour that you had described.

I vaguely recall that MS Word moved to OLE with version 6, and all organic chemists mourned the change, because we all had to go back to copying and pasting back and forth between Word and ChemDraw.





If you could duplicate the Word 5/ChemDraw 3 behavior I described above in the modern versions of Word, you would capture a large portion of the ChemDraw market. I know some people who still use Word 5 and ChemDraw 3, just so they don't have to copy and paste all the time.

OK, on my MacOS 10.3, using Marvin 4.2.0pre5, I can copy only either a bitmap image or a SMILES string into Word.





When I open up Preferences -> Copy, I see five options, but Chemical Structure is checked and grayed out, and OLE Object and Vector Graphical Image (EMF) are unchecked and grayed out. If I check both Plain Text (SMILES) and Bitmap Image, only the SMILES string is pasted into Word. If I paste the Bitmap Image into Word, I cannot copy it and paste it back into Marvin.





Perhaps ChemDraw uses the Vector Graphical Image also, and that's why, when you try to edit the picture in Word, Word warns you that the picture will lose vector information.





Again, it is imperative that one be able to copy a Marvin picture from Word back into Marvin. I'm about to start on a new book, and I want to use Marvin for my graphics, but if I have to save every graphic as a separate MRV file just in case I want to alter it, I'll have to go back to ChemDraw (ugh).

Please read the Marvin manual about copy/paste. Cut/Copy/Paste and Drag & Drop Functionality


It describes which copy options are available on which platforms.


Plain Text and Bitmap Image formats can be in conflict with each other by pasting into a couple of applications (e.g. some versions of MS-Word).


Marvin copy places structure to the clipboard in several formats and you can specify this settings through the "Copy" panel of the "Edit/Preferences" dialog.


The host application's business (where you paste the clipboard content) is which format prefers when retrieve data from the clipboard by pasting (if there are more options). MS-Office applications can accept several formats. You can choose the proper pasting format by using "Paste As Special" option in Word (if the default settings is not your preferred one).


You can read more about it in the mentioned document.





Currently, there is no vector graphics format under OS X that I can recommend you to copy it into MS-Word.


- EMF is a Windows native format. It is not supported under OS X.


- PDF would be a good choice because OS X systems "like" PDF but - as I know - Word can not paste PDF.


- SVG is a popular portable vector graphics format. But - as I know - Word does not support it in default. But I can imagine that there is SVG plugin for MS-Office (I've not tried it).


- Embedded Poscsript graphics (EPS) would be a good choice. As I know, EPS is insertable into Word. But the image is displaying only the printed paper. If the EPS graphics includes a preview (bitmap), this preview image will be visible in the Office document when you edit it.


Anyway, we are going to implement EPS export in Marvin because it would be useful for (La)TeX users.





Your wish (inserting an editable graphics object into Word which would be editable with Marvin directly by a popup sketcher) is a very difficult work. I suppose that it requires native (non-Java) code in OS X. I am not familiar with OS X programming, so I can not mesure it. But we are going to research the facility of this subject.

Here's some further information, from the ChemDraw manual:

Quote:

You can use the clipboard to transfer part or all of the information within an active document window between applications on the same computer or a networked computer. Use the standard "Copy-and-Paste" or "Cut-and-Paste" tools to transfer information to any application that supports these tools. The information is transferred as a ChemDraw drawing object.

Quote:

PICT files contain a QuickDraw representation of a ChemDraw drawing that can be used by various drawing applications. You can save a ChemDraw document in the PICT format so it can be opened by one of these other applications. The PICT file format contains ChemDraw structural information.

I copied a ChemDraw picture onto the Clipboard and opened a new document with it within GraphicConverter. GraphicConverter seemed to think that the document format was PICT. So, my guess is that the PICT format is the one that ChemDraw is using for pictures pasted into Word.

Quote:

To obtain the highest quality drawings possible on a PostScript printer, ChemDraw creates both a screen representation and a PostScript representation of your drawing.

Thanks.


I've suspected that the the structures source is stored as meta data in the image source.


Although, it is not editable, ChemDraw can retrieve structure from the image source when it is copied back to there.

So, can you do the same with Marvin?

No, Marvin can not paste images/graphics.

Can you modify Marvin so that it adds metadata when it creates an image, then extracts the metadata when the image is pasted back into Marvin?

We will investigate this facility.

Hi,





Any progress on integrating the MRV description into an image as metadata so that the image can be pasted into MS Word, copied, pasted back into Marvin, and edited? As I said previously, this feature is imperative if Marvin is to compete in word-processing applications. It does not appear to be available in Marvin 5.0.0.





-- Bob

Unfortunatelly, not. I can not promise to solve it in the near future.


Freehep API (that we use for creating EMF files) does not support to write any comment into the output file.


On the other hand, retrieving any comment from an EMF file is also a difficult question. It is a binary file that you can not parse if you do not know the exact syntax of the file. If we manage to store meta data in the EMF file, we would have to find a tool that is capable to retrieve meta data from the binary EMF.

That's really too bad. There are zillions of people out there who use chemical drawing tools (esp. ChemDraw) only for word processing applications, and you're freezing yourself out of that market by making it so difficult to edit Marvin pictures. And think about the companies that would want to be able to go to a single drawing tool, Marvin, for both their cheminformatics needs and their word-processing needs.

Tamas wrote:

Freehep API (that we use for creating EMF files) does not support to write any comment into the output file. On the other hand, retrieving any comment from an EMF file is also a difficult question. It is a binary file that you can not parse if you do not know the exact syntax of the file. If we manage to store meta data in the EMF file, we would have to find a tool that is capable to retrieve meta data from the binary EMF.

I looked up Freehep in Wikipediua, and it says that it supports creating PNG images. Then I looked up PNG, and it said that PNG can store textual metadata information. And I know that Marvin creates PNG images. So I guess I'm wondering why EMF is an issue. If it's just that you currently have EMF as the default format when the user copies a Marvin picture, simply provide an option for the user to set PNG as the default format.

Hi Bob,


Which platform we talk about? In Windows, EMF is the default copy format by Marvin.


In Mac, the bitmap image is default image format. I have believed you had talked about Mac.


By the way you can change the default settings in on the Copy panel in the Preferences dialog. Furthermore, by selecting the "Edit/Copy As..." menu item. You can give exactly in which format you would like to place the molecule to the clipboard, in the current case.


You can read about Marvin supported clipboard format and copy settings in the following document: http://www.chemaxon.com/marvin/help/datatransfer.html


Generally, we prefer vector graphics instead of bitmap image because graphics is scalable without distortion.





By the way, our PNG export does not use the Freehep API.


Indeed, PNG can store textual data. We will check how difficult is storing and retrieving textual data into/from PNG.

If you want to develop a solution just for me, a Mac-only solution would work. But I doubt you're interested in doing that, no matter how good a customer I am ;-), so I suggest you find an all-platform solution.





If you thought we were talking about a Mac platform, why did you bring up EMF? You said that you use FreeHep to create EMF files, and you couldn't easily store or retrieve metadata in EMF files. So I went to look up FreeHep in Wikipedia and saw that it could create output in other formats.





I only chose PNG as an example because I read on Wikipedia that it could store metadata. A Google search reveals that PDF can store metadata, too.

Just one more note.





For windows users, we recommend Marvin OLE objects to copy structures into MS-Office documents. Actually, OLE is a live object. It contains both the molecule graphics and source. The pasted OLE objects in an MS-Office document can invoke automatically MarvinSketch application to edit the encapsulated structure. After edit, you will see the updated image of the molecule in the document.





So, the problem exists on Linux and Mac platform where OLE is not usable. Currently, for Mac and Linux users, we can not provide any format where image and molecule source is encapsulated into the same object. But we are doing research in this subject.

Personally, I like SVG. It is an text based format (extension of xml) that describes a vector graphics. Since, it is an XML, inserting any comment into the source is easy.


We will investigate opportunities (which image formats can store textual data) and requests.

Hi, I'm writing a paper right now, and I am forced to use ChemDraw for my structures for the reasons discussed above. Going back and forth between ChemDraw and MarvinSketch confuses my fingers. (Commands and mouse actions give different results.) Any progress on incorporating metadata into Marvin pictures that are pasted into other applications?

We are still in the researching period. In a few of days, a new OS X test machine will have been received. I will do some test on it.


By the way, which version of Office for Mac do you use?

I use Office 2004.

Hi, I only want to underline the need for an editable/OLE embedding of Marvin for the MacOS version of MS Word (I'm using the 2008 Version). I'm writing a paper, too and want to use the Marvin applet on my Mac. This is still not possible, so I have to use the ChemDraw for it.

Hi,





This feature is already on our request list, having a quite high priority, but unfortunately there are others with even higher priority... the planning of version 5.2 is on the way, I will come back with the info whether we have capacity for this in the near future.





Best regards,





Akos

Hi Akos,





Any progress on this feature?





-- Bob

Hi Bob,





Sorry for the late reply; this topic was assigned to me, but I just came back from vacation where I had no internet connection...





Due to lack of capacity we could not implement this feature in 5.2. Presently, it is scheduled to 5.3; I hope we will have time for the implementation.





Best regards,





Akos

This subject has come up recently in this thread and this one as well, so I thought I would revive this thread.  Any progress in including the MRV as metadata in the figures that Marvin produces, so that when we copy those figures into another document, we can recopy them and paste them back into Marvin and edit them?  I'm talking about Mac users here, who don't have OLE.  

I've been requesting this feature for years.  I would really like to get away from ChemDraw completely.  Marvin has so many advantages over ChemDraw, but this is one glaring disadvantage that makes it extremely inconvenient to make the switch.  And I don't think it should be very difficult for you to do.

Since Marvin 5.5, the MRV source can be stored in Marvin created PNG, JPEG and SVG formatted images.

So when opening or pasting these images, the
molecule source is used (instead of trying to convert the image using OSRA).

Tamas wrote:

Since Marvin 5.5, the MRV source can be stored in Marvin created PNG, JPEG and SVG formatted images. So when opening or pasting these images, the molecule source is used (instead of trying to convert the image using OSRA).

That's great news!  And it will be even better when I can use Marvin 5.5 in MacOS 10.5 (see this discussion).

One question: You said "can be saved".  Does that mean that it requires special action on the part of a user, or does it happen automatically?

My colleague who can give detailed description about it is currently is not available. When he returns, answers all questions in this subject.

I'm one of the many Marvin fans who's still stuck with an ancient (2004) version of ChemDraw, and Word 2003, that I have to run in a Windows virtual machine on my Mac, whenever I need to prepare documents (in my case, patent applications) that call for more than a few chemical structures.

It's a bit astonishing that what I could do a decade ago under Windows, I still can't do on a Mac in 2011.  This is probably the single feature of ChemDraw that still induces people to shell out the ridiculous prices being charged for the program today.  I appreciate the challenges involved in bringing this functionality to Marvin, and I just want to thank and encourage the programmers who are trying to make it happen.

Hi,

it turned out, that the Office for Mac packages support the storage of molecule source inside an image, if it is in PICT, or in PDF format, so it is not enough to store the source in the formats we currently have this implementation. This is true for Office 2004, and office 2011, but it is not true for Office 2008.

We are keen on the solve this issue in the very near future, it is targeted to 5.8 and as far as i know, it is going to be released in 5.8, because most of the problems are solved regarding this development, and some implementation, and testing is remained for now. If the feature is ready we will let you know.

Regards,
Istvan