Dear Chimera developers,

 

Thank you for developing such a great and convenient software package.

Thanks!  I'm glad you find it useful.

Is there a way to use commands to select/identify those incomplete sidechains of a protein?

No, not without some monkeying around with Python.  But the monkeying around is fairly simple in this case.  Just take the Python code I've attached below and save it in a file that ends with ".py".  Then you can use the "open" command to open the file, which executes the code.  It will print the residues that are incomplete to the reply log.  The code is basically a straight copy of the same code from Dock Prep, with a few mods to make it work as an independent script.

In addition, is it possible to do the DockPrep job using commands instead of menu?

Again, not directly.  Is the purpose of this to execute Dock Prep in batch mode?  If so, this message from the dock-fans mailing list describes how to do that:

Thank you very much for your help!

You're welcome!

--Eric