[Chimera-users] Re: ribbons, chimera, and collagen

Eric Pettersen pett at cgl.ucsf.edu
Fri Jul 18 11:08:57 PDT 2003

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).


> 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

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