Hi Elaine, The command ribspline cardinal worked perfectly. Thanks a lot, Yehuda Halfon ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Wednesday, December 12, 2018 8:28 PM To: Yehuda Halfon Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] An oddity in ribbon. Hi Yehuda, In Chimera the default ribbon has a smoothed path, so it does not necessarily pass through the actual locations of the alpha-carbons (CA atoms). This is probably the reason for what you’re seeing — there is a sharp turn that gets smoothed to a shorter loop. Longer explanation here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset> You can instead make the ribbon go through the CA atoms, for example with command: ribspline cardinal … however, these will be very squiggly. For some compromise smoothing of strands only, could be something like: ribspline cardinal smooth strand <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html> You could also try ChimeraX, in which the default ribbons are at the CA atom positions except in strands. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 12, 2018, at 6:49 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi, I have an oddity when showing ribbon. When I show the loop (see figs) in ribbon I get the small thing in the middle and when I show it in atom the loop is longer. In coot the loop looks fine. Is it in the PDB? is in a chimera error? It only happens in this loop in this PDB. The same loop in other PDBs is fine. Thanks, Yehuda Halfon <coot.png><ribbon.png><atom.png>