[Chimera-users] An oddity in ribbon.

[Yehuda Halfon]

Hi Elaine, 

The command ribspline cardinal worked perfectly. 

Thanks a lot,

Yehuda Halfon
________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Wednesday, December 12, 2018 8:28 PM
To: Yehuda Halfon
Cc: chimera-users at 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 at 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>