COO- Group

I'm new to this software (v 5.11.5) and I'm trying to use an abbreviated COO- group, but I'm having no luck with it. I found the COOH group in the Insert->Groups menu, but that's about as far as I've gotten.

Dear smday55!

   If you are the administrator of a Marvin Sketch Applet, tha you can use the customAbbrevGroup option, you can find more information about it here.
   If you use the desktop version you can do else: Draw the desired molecule, make an SGroup name it, and (in expanded form) drag it to the template toolbar. Now you can easily add it to the canvas any time.

I hope, I could help:
Balázs

These instructions don't work for me.  I am not able to drag the expanded structure onto either the simple or advanced templates toolbar.

Is there a default.abbrevgroup file in MarvinBeans?

P.S.  I edited default.abbrevgroup in our server installation to recognize COO- with leftName \S-\nOOC.  I also created a CO2- shortcut group, but it appeared as CO^2- instead of CO₂^-.  I changed the name of the shortcut group to CO\s2\S-, but then Marvin did not retrieve it when I typed CO2- on the keyboard.  I suggest that Marvin ignore the escape characters when the user types a shortcut group name or when the groups are listed in the Groups... list.  

Okay, I was able to create the COO- group, but now, when I attach it to part o fa molecule, the bond attaches in the middle of the group name (at the middle O) instead of at the C where it should be, as shown below. I saw there was a previous thread on this same subject and the solution was to edit the .jar file, however I have the (pc) desktop version and am unable to find the file referenced in the previous thread. Below is the reply to the previous thread on this subject:

COO-    [O-]C=O    2    center=2

Hi,

You can use a
user defined abbreviated group as it is described in the documentation:

http://www.chemaxon.com/marvin/help/sketch/sketch-basic.html#User_defined_abbreviated_groups

To render it
correctly, you have to also define the connection point and  the „leftName” of your abbreviated group:

COO-     [O-][C]=O            2              leftName=-OOC

Then save it into
a file. The newly defined file must be named user.abbrevgroup and
should be put in the %USER_HOME%/chemaxon (on Windows) or $USER_HOME/.chemaxon
(on Linux, UNIX or OSX) directory in your file system. Note that Marvin gives
priority to the user-defined abbreviated groups and overrides the default after
redefinition.

Alternatively, you can use the attached file and if you wish
you can complete it with other groups.

Best Regards,

Efi

Hi,

I did all the suggestions/tricks you've mentioned already, and managed to have a proper
carboxylate group that I can use now - however I still have one more problem, maybe you can help.

An "extra" negative charge always stays outside of my contracted group,on both sides,
which seems to be some sort of renderering issue. This extra charge might be the [O-]
itself, but shouldn't the group name be shown while the group is in contracted mode instead
of anything else? When I expand it, everything is OK. I'm using the desktop version of MarvinSketch.

The line that I inserted to the "default.abbrevgroup" file looks like this:

COO-    [O-]C=O    2    leftName=\S-\nOOC

Thank you for your help!

Regards,
Bence

Hi,

This is a bug. Thank you for reporting it.

We will inform you when it is fixed.

Best Regards,

Efi