[Chimera-users] An oddity in ribbon.
meng at cgl.ucsf.edu
Wed Dec 12 10:28:41 PST 2018
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:
You can instead make the ribbon go through the CA atoms, for example with command:
… however, these will be very squiggly. For some compromise smoothing of strands only, could be something like:
ribspline cardinal smooth strand
You could also try ChimeraX, in which the default ribbons are at the CA atom positions except in strands.
I hope this helps,
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 at weizmann.ac.il> wrote:
> 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.
> Yehuda Halfon
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