Eric's fix hides the bonds that stretch across your simulation periodic box and the ribbon for one residue on each side of the jump. That won't completely fix the ribbons which use a spline guided by the ribbon C-alpha positions because the smooth spline distorts the ribbon for several several residues near the jump. If you hide the ribbon for just one residue on each side of the jump there will still be some rather distorted ribbon ends, but if you hide two residues on each side of the jump it mostly looks ok. Here are images hiding no ribbon residues, hiding 1 ribbon residue, and hiding 2 ribbon residues. Eric's Python script would need some more fancy code to hide two residues on each side of the jump.
Tom
Example of distorted ribbon where protein jumps from one side of periodic box to the other. Top shows full ribbon, middle shows ribbon hidden for one residue on each side of jump, bottom shows ribbon hidden for two residues on each sideof jump.
On Mar 25, 2024, at 6:19 PM, qz.chen--- via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yes, this can only affect part of the ribbon. Even the affected ribbon is only partially hidden. Anyway, thank you very much! _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
