[Chimera-users] What is the default of ribbon?

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 18 09:54:29 PDT 2016


Hi Root,
It is described in the “preset” documentation:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>

… specifically,
"Interactive 1 (ribbons) - shows most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.”

In other words, if the amino acid residue has any atom within 3.6 Å of what Chimera thinks is “ligand” or “ion” the whole sidechain will be shown, except any H atoms attached to C atoms.

You do not need to search on the net, you can just look at the manual included with your download, using menu: Help… Search Documentation.  For example, you could search for “presets” or “ribbon interactive preset”.  The information you found is explaining something different: why the backbone atoms are not shown.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Aug 17, 2016, at 11:13 PM, 郭尚哲 <b02b02049 at ntu.edu.tw> wrote:
> 
> Hi all,
> I have some pdb files of ligand binding protein structures, and when I check these structures with the ribbon diagram (Presets -> Interactive 1 (ribbons)) with chimera, it not only show the "ribbon" but also the sidechain of some residues. I would like to know why, so I search on the Net. And I just find the site below:
> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html
> It says "By default, when ribbon is shown for a residue, the mainchain atoms of that residue are hidden, except where bonded to other displayed atoms (such as the sidechain)."
> I can't get more imformation, and still don't understand.
> What is the rule chimera follow to show the sidechain of certain residues?
> Thanks,
> Root




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