[PyMOL] Gaps in cartoon representation due to non-continuous residue numbers

[Norbert S. <st...@bb...>]

Dear PyMOL experts,

in GPCR crystal structures it is quite common to have fusions with 
lysozyme or BRIL in the third intracellular loop. The residue numbers of 
the inserted domains are often incremented by 1000. As a result, the two 
residues at the fusion point jump from for example 223 to 1002. As a 
result, gaps exist in the cartoon representation at the fusion points. 
Increasing cartoon_gap_cutoff does not help as PyMOL rather connects the 
C- and N-termini of the GPCR fold. In stick representation, the peptide 
bonds at the fusion points are represented fine. I could not find any 
options like "cartoon_use_peptide_bonds" or  "bond_cartoon selection, 
selection". A workaround would probably be to renumber the residues of 
the fusion protein and use insertion codes, I did not try this yet. An 
example is pdb id 4eiy.

Is there a better solution, have I overlooked an option?

Best regards,

Norbert