in order to have sidechains be attached to your cartoon representation, the cartoons must not be smoothened.
set cartoon_flat_sheets, off
will do that. Be warned that your sheets will look like the ocean beyond the reef of Tunnels beach.
To get just a sidechain, type
show sticks, selection and not (n. ca,c,n and not pro/n)
or use the jiffy I wrote for this task:
You don't have to duplicate anything for what you want to do (show protein cartoon and sidechains and ligand spheres), you just have to define your selections properly. You might want to duplicate objects (I usually do.) in order to color more flexibly.
To display all atoms
show spheres, all
To hide them from the GUI, click on the objects in the list.
Hope that helps.
I have read the manual on how to have a cartoon representation of a protein and have one or more sidechains visible "and" connected to the ribbon (versus floating in space, see pg 39 manual). But I can not get that to happen following the instructions (using GUI or command line). Also, how do you get just the sidechain to be visible and not the backbone N and O? Can not find a way to select just one atom to turn them off, always get the whole residue using the GUI.
My goal is to have a cartoon representation of a protein with several connected sidechains visible with a ligand in the active site in spheres (CPK). It seems to me that I need to duplicate the structure and use the cartoon representation for the backbone/sidechains on molecule 1 and spheres for the ligand on molecule 2, is this necessary or is there another way? And is there a way to display all the residues/atoms in a structure and turn them on/off in the GUI?
Thank you for your help,
Gary S. Laco, Ph.D.
Assistant Professor of Biochemistry
Lake Erie College of Osteopathic Medicine-Bradenton
5000 Lakewood Ranch Blvd.
Bradenton, FL 34211