Hi Randy, You can force Chimera to treat collagen as helical without too much difficulty. First, select a chain or chains (either Select...Chain, or pick an atom or atoms in the graphics window and use up-arrow several times until the chain(s) are selected). Then use the selection inspector (Tools...Inspectors...Selection Inspector, or click the button showing the selection in the lower-right part of the Chimera window). Change what is being inspected to 'Residue' and then set 'in helix' to true. The problem is that the ribbons don't look very good (they're too "twisty") because it's not an alpha helix. Maybe Conrad can suggest something. I don't have any suggestions myself (I tried making them "strands" and that was pretty twisty also). --Eric
I'm trying to make a ribbon plot of collagen using chimera, but it doesn't recognize collagen's secondary structure. Can I just tell it to make a ribbon with the backbone atoms (or peptide bonds), and not worry about what kind of secondary structure it really is? If so, how? Have a nice day, Randy