Help Creating -OR Group Abbreviation

I have been struggling with this for some time. I am using MarvinSketch for Mac.

I need to create an OR group abbreviation. Having a R-O bond is unacceptable to my advisor. I have created the user.abbrevgroup file and I have been able to make a COO- group as per these threads. However I am unable to define my own groups. I have noticed there is some kind of syntax to follow in the text, but I can't figure it out. I have tried the following:

OR	[O][R]	1	leftName=RO
OR	O-R	1	leftName=RO

I can see when trying to type the abbreviation in MarvinSketch that the abbreviation is recognized, but it is never put onto the cursor. I can never type the whole abbreviation. It is always cancelled and I end up with a standard O or R on the cursor. The documentation is very sparse and all links in this forum point to 

How can I make an OR group? Where can I find a syntax guide for how to write these abbreviation lines?

Sorry for the late reply.

You can find the description of Chemaxon's abbrevgoup file format in this section of our User's guide.

Please find  below the attached file which contains the requested OR abbrev group as an O atom with OR alias atomlabel.

If you need such groups only occasionaly, you can use Alias atoms. Please find more information how to create alias atoms here.

Should you need any further information, please do not hesitate to contact us.

Best regards,

Nikolett MIhala

Excellent. I will look into this soon. Thank you for the reply. You're a saint.

nmihala wrote:

Sorry for the late reply. You can find the description of Chemaxon's abbrevgoup file format in this section of our User's guide. Please find  below the attached file which contains the requested OR abbrev group as an O atom with OR alias atomlabel. If you need such groups only occasionaly, you can use Alias atoms. Please find more information how to create alias atoms here. Should you need any further information, please do not hesitate to contact us. Best regards, Nikolett MIhala

Thanks for the file, Nikolett, but I find I have the same problem as before. I try to type in the abbreviation with the keyboard. I see the OR group pop up in the shorthand display in the top-left corner of the canvas but I can't actually put the group on the cursor. Am I doing something wrong in trying to use it?

No, it should work as you described it.

Would you be so kind as to try this newly attached file?

If it does not work, could you specify what OS X environment do you use, please?

I hope this simplified file helps.

Best regards,

Nikolett

Ahh. That one works just fine. I am reading into the syntax here with the links you provided. I don't understand it yet; it's more complicated than I thought. 

Thank you for all your help!

FWIW: I'm using a Macbook Pro 12,1 running OSX 10.11.6 and MarvinSketch 6.2.2

This is good news.

A very basic process to create user-defined abbreviated groups is:

1. Clear the canvas.


2. Draw the structure.


3. Select the structure and using the 'Create Group' dialog name it.


4. Add attachment point(s). - Optional  (Select the atom and click the Add S-group attachment from the contextual menu.)


5. Copy
   the content of Edit<Source<View<SMILES<Chemaxon SMILES
   Abbreviated Groups dialog to a text editor. (For more options see the abbreviated group file formats.)
   
   
   
   1.  If you do not have user.abbrevgroup file than save it to your Chemaxon folder
   
   
   2. If  your already has created user-defined abbreviated groups  copy the content of the dialog box to your file.
   
   

I think we will release a tutorial video about it some time next year. We will get in touch with you when it is available.