I’m looking for a way to label each atom with an arbitrary label. In
the label engine, there is an option for custom data. By default, this
shows the atom symbol. Is it possible to change this? If it is, it is
not obvious how. Maybe put a button in the settings dialog?
Dave
You can do it with the selection tool (F11), right click on the atom and choose ‘Change label’. Not the most intuitive way, also because the ‘custom data’ option in the labels is misguiding imo. But at least it can be done.
[Edit] Mmmhh, the header on the comment says “9 years later”… Didn’t see that.
I still appreciate the reply. 
I am still to new at this to know whether this is available, but it would be of value to be able to label chirality (centers, axes, whatever). Centers are clearly the most important. It would be nice if you could click on something and have the chiral centers identified as R or S. Is that available in the software?
John
If you install the rdkit plugin, the “Assign Stereochemistry” should use RDKit’s code should create “R” and “S” custom labels for atoms.
If you’re aware of other packages that can assign chiral labels, it shouldn’t be hard to adapt to a plugin.
I installed the rdkit plugin and gave it dehydromethionine as a test (which has an S center). I clicked on rdkit>assign stereochemistry. It came up with a box saying “Processing Assign stereochemistry” and that box has been there for over 20 minutes with no assignment. It looks like some sort of infinite loop. Appimage in Fedora version. I then tried it in windows 10 and got the same thing.
John
Hmm. I’m getting the same thing on my Mac. I’ll hopefully have some time tomorrow. The good news is it should be an easy fix and you can install the updated plugin.
