Pointing to a certain atom symbol in abbreviated groups

Hi,

I'm looking for an option to point to a certain symbol (of a bonding atom) of an abbreviated group. For instance, I created a abbreviated group COO- for the carboxylate ion. When I contract the group, the bond points to the middle of the abbreviation (COO-), but it should point to the "C". How can I manage this?

There is already a carboxyl group under "Insert -> Groups" and the abbreviation COOH is arranged correctly.

I'm not very experienced in using MarvinSketch, but I hope there is a quite easy possibility to solve my problem. I've read something about this problem in the documentation (http://www.chemaxon.com/marvin/help/formats/abbrevgroup-doc.html), but I have no clue where the file "default.abbrevgroup" is located or where it has to be placed. I'm using MarvinSketch Version 5.8.0 on Mac OS 10.7.3.

Thanks in advance,

Diego.

Hi Diego,

unofrtunatelly in the current versions you can not easily set the label center property on a SuperAtomSgroup. The only way to create such a group you want is to edit the default.abbrevgroup file in your marvin installation.

If you want to do so, you should locate the MarvinBeans-templates.jar file on your system it should be in the marvin_installation_dir/lib directory, the default.abbrevgroup file is inside the jar, you can edit the jar freely, since on a desktop installation there is no need to sign the jars it is allowed to modify its contents.

You should place this line into the file:

COO-    [O-]C=O    2    center=2

please be aware of the rule that the delimiter character is tab in the abbrevgroup file format, i used some spaces in this example line.

After you have edited the file, you can reach the COO- group by typeing.

In 5.10 we are planning to define an easier way to create such groups either in a separate file and maybe also from the UI.

I hope this helps.

Regards,
Istvan

Hi,

I'm having some challenges editing the default.abbrevgroup file inside the jar (I'm not an expert in this area).

1. I can open the MarvinBeans-templates.jar by converting to .zip and opening using Archive Utility. 


2. Then I can edit the default.abbrevgroup text file (in my case adding 'CF2 FCF 2'). I save this.


3. Then I compress the folder and replace the MarvinBeans-templates.jar


4. Upon opening MarvinSketch I lose all groups (like CF3 which is a default group).

Do you think that you could help point out what I need to do to add my user defined abbreviations. This is a very helpful feature that I only recently found existed.

Thanks,

Chris

(Marvin 6.2.1 on OS X 10.9.2)

Hi Chris,

Since 2012, there is a more convenient way to add abbreviated groups to the default abbreviation collection. For detailed information please visit http://www.chemaxon.com/marvin/help/formats/abbrevgroup-doc.html ("Extending the built-in abbreviated groups" section). 

Please let us know if you need further assistance.

Regards,
István Őri 

Thanks for the quick reply. I presume this is the relevant information I need:

"A user can define abbreviated groups to be used in MarvinSketch in a file called user.abbrevgroup. This file has to be placed in the chemaxon settings directory that is located in the chemaxon or .chemaxon folder inside the home directory of the user."

I tried this originally I thought by opening Applications folder - ChemAxon folder - MarvinBeans folder - lib folder - MarvinBeans-templates.jar. After converting to MarvinBeans-templates.zip and making changes to the default.abbrevgroup text file I compressed and converted back to .jar MarvinSketch abbreviations no longer work.

So I assume that I must be looking in the wrong place for the user.abbrevgroup file. Could you send more specific instructions to find it? I have search for it on my computer for Home folder in Finder but nothing comes up.

Thanks,

Chris

Dear Chris,

On your mac there is a home folder usually with your username, which has a hidden folder named .chemaxon (in your finder might not see it, you'll have to adjust the settings to see hidden folders) , if you have sketch installed to your computer. You'll have to navigate there and create the user.abbrevgroup text file. After adding the abbrevgroups by the proper format (defined upper), you can use them in sketch, as you would use any other predefined abbrevgroup. 

 

I hope this helps, and if you need further advice please feel free to contact us.

 

Tamas Fazekas-Vigh