Marvin 5.0.0 problem

Just installed Marvin 5.0.0, and already a problem:

Code:

chemaxon.formats.MolFormatException: The markup in the document following the root element must be well-formed.    at chemaxon.marvin.io.formats.cml.MrvImport.readDocument(Unknown Source)    at chemaxon.marvin.io.MRecordImporter.readDoc(Unknown Source)    at chemaxon.marvin.util.MolLoader.a(Unknown Source)    at chemaxon.marvin.util.MolLoader.run(Unknown Source)    at java.lang.Thread.run(Thread.java:613)

The error occurs here right when the applet is loading. The call to the applet reads:

Code:

<script type="text/javascript">    msketch_name="mechapplet";    msketch_begin("/nosession/marvin", 500, 400);    // arguments: CODEBASE, WIDTH, HEIGHT    msketch_param("preload","SmilesExport,MolExport,Parity");    msketch_param("molbg", "#ffffff");    msketch_param("mol", "");    msketch_param("atomsize", "0.4667");  // (30*parameter = points)    msketch_param("scale", "32");  // C-C bond length in pixels    msketch_param("abbrevgroups","ACE.abbrevgroups");    msketch_param("reactionSupport", "false");    msketch_param("xtmpls", "chemaxon/marvin/templates/mechTools.mrv");    msketch_param("extraBonds","wedge,either");    msketch_param("implicitH", "heteroterm");    msketch_param("lonePairsVisible", "true");    // msketch_param("atomNumbersVisible", "true");    msketch_param("sketchAnyBond", "dashed");    msketch_end(); </script>

In addition, our custom toolbar buttons are not appearing. See here to see the buttons we have added.

Dear Bob,





earlier the xtmpls parameter were used to achieve a kind of customization.





Marvin 5.0 offers full GUI customization which can give better result than the xtmpls parameter.


The attached images show examples of a similarly customized gui.





If this solution is suitable for you, we can go through the details.





Kind regards,


Judit





P.S. We'll get back about the xml reading exception soon.

Sure, this solution is fine. But is there any reason you did not make Marvin 5.0 back-compatible with the old "xtmpls" formulation?





Can you tell me where to look for documentation on how to convert our old custom buttons into new ones? Also, the ring templates on our own page (pyrrole, benzene, etc.) look different from the ones in your picture. Do we need to change them, too?

Bob, please send us the MRV file where this problem is occurred (mechTools.mrv).

I'm attaching two .mrv files, each of which is used in different contexts in ACE to add buttons and templates.





I came across your Configuration and Customization pages for Marvin 5.0.0, but they appear to be directed only at the user. Can we still use the JSP page to specify a configuration server-side?





Also, on this example page, you talk about adding extra wedge bond buttons to the toolbar using the xtmpls parameter, but no extra buttons appear in the applet. I suppose you haven't got around to editing this page yet.

I'm also wondering where is that wonderful dative bond type that you showed me some time ago? I don't see it on the Marvin demo page.

Yes, the configuration can be made server side too, and we'll give documentation and full support to achieve it. We'll put a notification here when an example is ready.





The template handling was changed a bit in 5.0, as shown here, but there are some more improvements that still need to be done.


We also intend to recover the xtmpls parameter support in the near future.

Hi Bob,


Thanks for the files.


Since Marvin 5.0, the root tag is obligate in MRV and CML. It means that there are more than one <MDocument> in an MRV file, <MDocuments> tags have to be enclosed in a root <cml> tag.


To provide backward compatibility with old MRV files, current Marvin accepts old MRV files (with multiple MDocument records) if the file looks like this:

Code:

<?xml version="1.0"?> <MDocument> ... </MDocument> <MDocument> ... </MDocument>

Furthermore, MRV import accepts any file that begins with a <cml> tag:

Code:

<?xml version="1.0"?> <cml>

In your example, a comment (<!-- ... -->) is in the second line (after the xml header) where the root tag is expected.


There are two ways to correct files:





1. Enclose everything (after the xml header into a <cml> tag.

Code:

<?xml version="1.0"?> <cml> <!-- rectangle, reaction arrow, textbox --> <MDocument> ... </MDocument> <MDocument> </MDocument> ... </cml>

2. Delete the comment from the second line, (the <MDocument> tag has to follow the xml header).





The first solution is recommended because it gives a well-formated xml.


Both Marvin 4.1.x and 5.0 can import the corrected files.





Of course, we will fix this backward compatibility issue in the near future.

Judit wrote:

Yes, the configuration can be made server side too, and we'll give documentation and full support to achieve it. We'll put a notification here when an example is ready. The template handling was changed a bit in 5.0, as shown here, but there are some more improvements that still need to be done. We also intend to recover the xtmpls parameter support in the near future.

Glad to hear it. Another thing to add to your to-do list: The command,

Code:

msketch_param("tmpls7", ":Conformers:chemaxon/marvin/templates/conformers.t");

appears to have no effect in Marvin 5.0. When I go to My Templates, I do not see any conformers. I'm attaching the relevant file, though I needed to change the extension to MRV because this forum doesn't allow a .t extension. BTW, I have no objection if you want to include this file as one of your standard template sets.

bobgr wrote:

I'm also wondering where is that wonderful dative bond type that you showed me some time ago? I don't see it on the Marvin demo page.

If you mean dative bond as a coordinate bond, you can draw it with the bond drawing tool or change the bond type to coordinate bond with Bond/Type/Coordinate from main menu and contextual menu.





Best regards,


Erika.

Thanks, I found it. Your Marvin demo page has an explicit list of bonds, and the dative bond is not included, so it doesn't show up as an option in the buttons.

Fixed the reading of MRV starting with comments (synthTools.mrv and mechTools.mrv). It will work in 5.0.1.

The tmpls parameters will be corrected along with the xtmpls parameter.

Hi Bob,





description and some brief examples are available showing customization made on server side: http://www.chemaxon.com/marvin/help/sketch/gui/customization_server_side.html


Please let us know how you succeed with this document.





I suppose you will also need help to find the new buttons in the lists that can replace the old ones. For example Insert 1 Electron Flow Arrow can be found in the Insert Graphics category, named 1 Electron, as the attached image shows.


Please tell us if they are easy to find or not. Would an extract be useful about the most frequent commands? Do you have any ideas how could this be more easy to use?





Kind regards,


Judit





P.S. the demo page showing bond types is updated with the coordinate bond. Thank you for the notice.

Judit wrote:

Hi Bob, description and some brief examples are available showing customization made on server side: http://www.chemaxon.com/marvin/help/sketch/gui/customization_server_side.html Please let us know how you succeed with this document. I suppose you will also need help to find the new buttons in the lists that can replace the old ones. For example Insert 1 Electron Flow Arrow can be found in the Insert Graphics category, named 1 Electron, as the attached image shows. Please tell us if they are easy to find or not. Would an extract be useful about the most frequent commands? Do you have any ideas how could this be more easy to use?

The Customization dialog box seems to me to be pretty straightforward to use. I don't have any complaints about it.





Thanks for posting the server-side customization documentation. It doesn't look too difficult to do. However, the new methods are quite different from the Javascript msketch_param() calls, and, since we have quite a few pages where we call MarvinSketch, and each and every one of them will have to be updated to one of several new configuration files if we move to Marvin 5 now, I think we'll wait until Marvin recovers the xtmpls parameters before upgrading to Marvin 5. Then we can experiment more slowly with the new customization methods.





I like the ChemDraw-like and ISIS/Draw-like options. I guess we'll have to make an executive decision about how we want Marvin to look when students start using it.





One thing I've noticed is that the toolbars and buttons require more space in the newer layouts. We may have to do some serious redesign of ACE's layout if we decide to go with one of the newer Marvin layouts. I realize that we can stick with the "classic Marvin" layout.

I am playing with the sketch applet in Marvin 5.0. I am developing tutorials for organic chemistry students and am doing the development on a new iMac.





I do not need all of the items in the toolbars and have found the method for setting up a page like I want it from the GUI. However, I do not see how to save that customization and make it load in subsequent, or how to specify it in javascript. I have followed this discussion, but I do not find the files you speak of, and cannot see where I can generate an appropriate file to save.





It is interesting that Safari will reload the applet with the same customization -- probably from cache. But it does not live for other browsers -- which again is reasonable if it is coming from cache.





In the process, I have found a couple of bugs. I wanted to get an IUPAC name and was told I did not have a license to do so. OK I can live with that. But subsequently anything I selected from top toolbar gave me the same message about the naming license -- even though the selections were totally unrelated.





The Javascript parameter does not seem seem to put the up and down bond icons in the tool bar. I succeeded in doing so using the customization routine in the GUI. However, they were not active, unless I selected the whole molecule, at which point I could change all bonds to up or down -- which is not what I wanted.

Hello,

Quote:

but I do not find the files you speak of

you mean the configuration file: customization.xml?


It should be at

Code:

/Users/username/.chemaxon/5.0.0/customization.xml

You can specify it in javascript like:

Code:

msketch_param("menuconfig", "http://example-server.org/marvin/configuration.xml");

You are right about the IUPAC naming problem. It will be fixed with the next patch release (around mid-February).





Yes, the xtmpls parameter is currently out of order, but it will be fixed soon.


The problem with the up and down bonds can be simply solved. There are 2 different bond actions, please try the one found in the Insert Bond category instead of the Bond Properties category.





Please let us know how you succeed.


Kind regrds,


Judit

Judit wrote:

Hello, Quote: but I do not find the files you speak of you mean the configuration file: customization.xml? It should be at Code: /Users/username/.chemaxon/5.0.0/customization.xml You can specify it in javascript like: Code: msketch_param("menuconfig", "http://example-server.org/marvin/configuration.xml");

OK. I find it. So this serves on the client side. What will happen when I move this to the campus server? Where will the file be on the campus server?

Quote:

You are right about the IUPAC naming problem. It will be fixed with the next patch release (around mid-February). Yes, the xtmpls parameter is currently out of order, but it will be fixed soon. The problem with the up and down bonds can be simply solved. There are 2 different bond actions, please try the one found in the Insert Bond category instead of the Bond Properties category.

Actually, I defined the up and down bonds in my customization file. I will add it for your perusal. It did not work the first time. After I restarted the browser, it worked.





I am also having some difficulty with some browsers having to be restarted to reload the applet. I am still playing with that.

pbays wrote:

OK. I find it. So this serves on the client side. What will happen when I move this to the campus server? Where will the file be on the campus server?

You can upload it to anywhere on the server, but the URL has to be exactly specified with the menuconfig applet parameter.

Dear,


>


> I installed JChem on Mandriva linux and about installation I've not had


> any problem, but I can't find the jchem icons on my desktop, and I can't


> find also the icon to run the software inside to the folder. I already


> installed last version of java.


>


> I'm looking forward your news


>


anton

The Linux installer of JChem does not place any icon to the destkop.


You can launch JChem applications by scripts that you can find in the jchem/bin directory.

In the next release, the linux installer will be able to place icons to the desktop.

The backward compatibility of MRV import has been improved.


Marvin 5.0.1 will accept old MRV files with comment. It means the such kind of old MRV files can be imported:

Code:

<?xml version="1.0"?> <!-- This is a comment --> <MDocument> ... </MDocument> <MDocument> ... </MDocument>

Dear Bob,





Marvin 5.0.1 is released, and tmpls, ttmpls, xtmpls parameters do work again.


However there is a slight modification in behavior, for the details please see http://www.chemaxon.com/marvin/help/developer/templates.html





Another change that can be interesting to you is the new drop-down list of toolbars. This allows using the window size of the previous versions without loosing functionalities by hidden buttons.





Kind regards,


Judit

New Version is OK, and easier to use.

Judit wrote:

Dear Bob, Marvin 5.0.1 is released, and tmpls, ttmpls, xtmpls parameters do work again. However there is a slight modification in behavior, for the details please see http://www.chemaxon.com/marvin/help/developer/templates.html Another change that can be interesting to you is the new drop-down list of toolbars. This allows using the window size of the previous versions without loosing functionalities by hidden buttons. Kind regards, Judit