Dear Miao, Details depend on whether the cartoon part is on the N-term side (lower residue numbers) or C-term side (higher residue numbers). If both, then you can combine the following answers. If cartoon is on the N-term side, for example, residues 1-9 of 1gcn, you could show the C atom of the last cartoon residue (so that there will be bond to N of the first atoms residue): open 1gcn hide cartoon cartoon :1-9 suppress false show :10-29 atoms show :9@c -- or maybe more atoms from residue 9 (if that looks better), for example -- show :9@c,ca The "suppress false" is important because it allows showing backbone atoms for the same residues that are also shown as cartoon. The full option name is "suppressBackboneDisplay" but you can use the shorter version. See the help if you want more explanation: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> If cartoon is on the C-term side, for example, residues 10-29 of 1gcn, you could show the N atom of the first cartoon residue (so that there will be a bond to C of the last atoms residue): open 1gcn hide cartoon cartoon :10-29 suppress false show :1-9 atoms show :10@n -- or maybe more atoms, as above -- show :10@n,ca The reason to also show CA atoms from the cartoon residues is that the cartoon position will be close to CA but it might not be close to N or C. If the N or C is not close to the ribbon, you may see a small cone that connects it to the ribbon, which we call a "tether" .... and you can change tether color, shape, etc. or make it invisible (opacity 0 which means completely transparent) with the command "cartoon tether": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 3:25 PM, Zhang, Miao via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Sir/Madam
When I made a figure with part of the chain shown as sticks, and part of it shown as cartoons, there is a gap between the cartoon and sticks. Is there a way to fix it?
<image001.png>
Best,
Miao