Adding custom atom labels such as CF2

I am trying to draw the structure C6H5-O-CF2-CF2-CF3 but I am unable to figure out how to relabel a CH2 to a CF2 and have it displayed normally. CF3 is in the library of groups that can be added. If I add the group as alias, it is hidden because I want implicit carbon atoms hidden. If I add it as a psuedo, it is italicized and looks terrible. I am rather new to Marvin - am I missing an obvious way to do this? Is there a way to add atoms/groups to the library? I've been all over the forums and through the help files trying to figure it out.

The easiest way if you add C5H6 and CF2 as a custom defined abbreviated group. ( You can find the related documentation here http://www.chemaxon.com/marvin/help/sketch/sketchbasic.html#User_defined_abbreviated_groups)

I am attaching the user.abbrevgroup  file which you need, please put into your userhome/chemaxon directory. I am also attaching the mrv file with the requested structure.

Best Regards,

Efi

Thanks for the help! It took me a little bit to figure out the format for entering the user defined groups, but I'm off the the races now. The bonds keep overlapping my abbreviations, but I expect I can figure out that formatting.

I have one remaining question on the subject. With the CF2 abbreviation correctly coded as you showed me, I can only create branches with CF2 or replace terminal atoms with CF2. In other words, I can't draw propane and directly  replace the middle hydroncarbon with CF2. Is there a way to do this or must I continue drawing a bond, adding CF2, drawing another bond, adding the CF2, and so on?

Thank you so much for your time!

It is a bug indeed. Thank you for reporting it. I create a task about it in our issue tracking system.

Best Regards,

Efi

Hello, I have exactly the same problem with displaying CF2 groups.

I am afraid, I do not understand where to put the user.abbrevgroup file. Can someone please explain it a little bit more in detail?

I am using Mac OS X (10.9.1) and MarvinSketch 6.1.4

 

Thanks!

You should copy it to the chemaxon folder, which is a hidden folder in your home folder. (If you have any further question about how to handle hidden folders please look at this link: https://discussions.apple.com/message/24295922#24295922 )

Regards:
Balázs 

Thanks a lot, I found it.

Hello,

meanwhile I found time to experiment around with user.abbrevgroups and some things work quite well.

But I noticed there is still a problem with the above mentioned CF2 group: The .abbrevgroup file above contains

CF2    FCF    2    2

For me it is not possible to replace CH2 with CF2 in a chain with this code. Instead the structure editor wants to add CF2 similar to CH3 resulting in a branched structure.

I managed to make it look better changing the line to

CF2    FCF    3    2

Anyway, the chemistry is wrong when I expand the group.

What is the solution to achieve both, being able to replace CH2 by point&click and having the right structure when expanding it?

 

Please have a look at the attached PDF

 

Thanxalot!

Dear Zoopismo,

for CF₂ is your first abbrev.group is correct as both attachment points are positioned on the carbon atom.

Unfortunately the expexted behaviour is sprouting because the methelene group can be further substituted, but if you change the -CH₂-  to an O (oxygen atom) you can replace it by your CF2.

If there are more than one attachment points please always consider their position as bonds are formed according to the attachment point  number.

Best regards,

Nikolett Mihala