Labeling of molecule

I wonder if there is any way how to attach a "neutral" label to the molecule. I mean a tag (e.g. descriptive text) that will be firmly connected to the molecule but not as a flag via chemical bond to a particular atom and certainly will not influence the atom/bond count.

Hello, what about creating a group? Select the molecule/fragment you want to attach a label to, right click with the mouse, select create group and type in the name you want to use.

Good idea. You mean to handle the molecule as superatom with descriptive text within LABEL field (?)

Exactly. There are other benefits (contracting the molecule, using only a fragment of a bigger structure, etc). I just do not know whether is it OK for you. If you check the .mrv file, it is stored as a "molecule property" so not attached to atoms/bonds, but to a fragment.

szilva wrote:

If you check the .mrv file, it is stored as a "molecule property" so not attached to atoms/bonds, but to a fragment.

That is good but apparently the information cannot be passed to mol or sdf; it is present in the mol or sdf file but not recognized by mview and/or msketch.

jirikrechl wrote:

That is good but apparently the information cannot be passed to mol or sdf; it is present in the mol or sdf file but not recognized by mview and/or msketch.

If not ungrouped, the superatom S-groups should be preserved in mol and sdf formats, but expanded superatom sgroups are not visible using mview. (The mouseover highlighting behaviour does not work there.)





Attaching data may be a better alternative for you then. Select the molecule to be labeled, right-click on the selection and select Add->Data... from the popup menu. In the dialog, fill in the data field name and value. (The value will be displayed, and the label is relocatable.) Attached data can be saved in mrv and mol/sdf formats.





You may also use Insert->Text from the main menu, but those text boxes can only be saved in mrv format.





Best Regards,


Szabolcs

Szabolcs wrote:

Attaching data may be a better alternative for you then. (...) Attached data can be saved in mrv and mol/sdf formats. Szabolcs

The formats mol/sdf do work but when I save it as extended mol (my preference) I cannot open it further neither with mview nor msketch.

It seems to work for me. Does it give an error message?





Which Marvin version do you use?

Szabolcs wrote:

Which Marvin version do you use?

4.1.0 for both the mview and msketch.

It seems to work for me. Does it give an error message?





No error message. It simply does not open the file. Example attached.

Thanks for the test file. It seems that there is a problem with attached data and groups in R-group definitions in case of the extended molfile. We will check what's wrong.

Dear Jiri,





Marvin 4.1.5 will contain the bugfixes for the above mentioned problem (related to extended molfile import/export of groups in R-group definitions). Unfortunately there were bugs in the extended molfile export so your "test.mol" file is corrupt.


The structure should be redrawn and saved again with Marvin 4.1.5. Here I attach test.mol in a proper form.





If you have more extended molfile that you can not import, let me know.


Marvin 4.1.5 will come out in early January.





Best Regards,


Erika