jiywang3
commented
1 year ago I think when you click the menu "Select > by Distance", you select "chemicals" as the first set, and "non-selected" as the second set. Since all are selected at the beginning, "non-select" is empty. So nothing is selected. iCn3D selects all residues when nothing is selected.
You can simply change the second set as the whole structure, i.e., the set "5C45". Here is the URL to produce what you want: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?FpiAYYkmQa96z9Eo7
I made a structure annotation and wanted to share the link, the full structure is displayed instead of my annotation.
Short form: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?jj3vLHn2W9iYzv8T6 or
long form: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=5C45&bu=0&date=20230203&v=3.21.2&command=set shininess 60; set light | light1 0.8 | light2 0.1 | light3 0.2; style nucleotides lines; style nucleotides lines; select zone cutoff 4 | sets chemicals non-selected | false; select zone cutoff 4 | sets selected non-selected | false; select sets chemicals; reset; reset; style nucleotides stick; style nucleotides stick; select zone cutoff 4 | sets selected non-selected | true; select zone cutoff 4 | sets selected non-selected | true; select zone cutoff 4 | sets selected non-selected | false; select zone cutoff 4 | sets selected non-selected | true; select sets sphere.51B:51B1004-4A; hide selection; hide selection; select zone cutoff 4 | sets selected non-selected | true; select zone cutoff 4 | sets selected non-selected | false; select sets chemicals or sphere.51B:51B1004-4A; style water dot; style water dot; color atom; color atom; set mode all; set mode selection; select sets chemicals or sphere.51B:51B1004-4A; hide selection; select sets chemicals or sphere.51B:51B1004-4A; show selection; select sets chemicals; style chemicals ball and stick; style chemicals ball and stick; contact map | dist 8 | type cbeta; add residue labels; add residue labels; select sets sphere.51B:51B1004-4A; add residue labels; add residue labels; select sets chemicals; style chemicals schematic; style chemicals schematic; select sets interface_all; delete selected sets; select sets interface_2; delete selected sets; select sets interface_1; delete selected sets; select sets nucleotides; show all; select sets !X or !Y; style nucleotides o3 trace; style nucleotides o3 trace; color 808080; select sets sphere.51B:51B1004-4A; style nucleotides stick; style nucleotides stick; color atom; color atom; select sets|||{"factor":"0.3908","mouseChange":{"x":"0.000","y":"0.000"},"quaternion":{"_x":"-0.4866","_y":"-0.7387","_z":"0.08752","_w":"-0.4581"}}
desired display:
What I got: