Dear all: I am facing a display issue in pymol. In my structure, there is a nucleic acid chain with some monomers which are modified nucleotides built in scketcher of ccp4 suite. However, When I showed the structure in pymol as cartoon, the nucleic acid chain was discontinuous where the monomers are placed. I could not get a intact nucleic acid chain except setting the cartoon_nucleic_acid_mode value to 1, with the backbone passing through ribose C3' atoms.
I tried to add SEQRES lines into the pdb file according to the pdb instruction, but it doesn't work if I want the backbone to pass through phosphorus atoms. May I get some suggestions from you? Although it's not a big problem, it's really painful. Thanks a lot and best, Xiaoming
