[chimera-dev] Changing guide atom

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 17 09:48:39 PDT 2008

Dear Patrick,
I can't answer the Python question, but I recommend using the Ribbon  
Style Editor (under Tools... Depiction) to do this instead of  
changing code.

In Ribbon Style Editor, see the "Residue Class" section.  Instead of  
changing the Chimera defaults for amino acids and nucleotides, you  
can make your own new classes, name them, and apply them selectively  
by name. The documentation also explains more about how ribbon guide  
and orientation atoms are used:

I believe you cannot use the same atom as both guide and orientation  
atom.  That may be the problem in your case, since the default  
peptide orientation atom is O.  You may want to try some different  
combinations of which backbone atoms are used as guide and orientation.

Some previous posts about ribbon residue class:

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

On Oct 17, 2008, at 3:50 AM, Patrick Ladam wrote:

> Hello list,
> I'd like to change the guide atom in res.ribbonData to use
> O instead of CA as an example.
> Here is what I did:
> for r in mol.residues:
>   for a in r.atoms:
>     if a.name == 'O':
>       r.ribbonData.guide = a		# Set O as guide Atom
>       if r.isHelix: 			# Update the display
> 	r.ribbonDisplay = True
> 	r.ribbonDrawMode = chimera.Residue.Ribbon_Round
> This does not seem to redisplay/recompute the helix through O Atoms.
> I am not confident with the way I altered the guide Atom or is it
> another problem like updating the ribbon or so...
> If someone can help...
> Thanks to all
> PL

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