Ticket #15360: cyclic_ribbon.cxc

# Commands to make a ribbon of a cyclic peptide that appears closed for publication images.

# Chain A is cyclic and chain B is not cyclic in this structure
open diffused_binder_5_cyclic_325.pdb

# Make a second copy to extend chain A.  The combine command with one model makes a copy.
combine #1

# Delete chain B of the copy since only chain A is cyclic
del #2/B

# Renumber the residues of the copy so they can be appended to the original model.
# The cyclic peptide chain A is residues 1-16, so make these extra ones 17-32.
renumber #2 start 17

# Now combine the original atomic structure and these extra residues
# The retainIds option means to keep both chain A as a single chain A instead of renaming one.
# The close option means close the original two models leaving only the combined one as #1.
combine #1,2 retainIds true close true

# Now hide 8 residues on each end of the cyclic peptide.
# We added these just to get the ribbon to smoothly join itself.
hide #1/A:1-8,25-32 ribbon

# The chain A ribbon inherited the colors from the original two models, so recolor it.
color #1/A pink