[Chimera-users] Adding arrowheads to protein helix ribbons?

[Elaine Meng]

On Apr 15, 2008, at 1:49 AM, Peter Knight wrote:
> I am dealing with antiparallel alpha helices in helix bundles. It  
> would be very useful to be able to show the polarity of each helix  
> in ribbon display by adding an arrowhead to the C-terminal end.  
> This is the default for beta strands. Is it possible to add such an  
> arrowhead in Chimera?
>
> A clunky workaround that occurs to me is to designate the last  
> residue of each helix as beta structure. Has anyone tried this:  
> does it work?
> Thanks,
> Peter Knight
> University of Leeds, UK

Hi Peter,
There is no provision in the Ribbon Style Editor for putting arrows  
at the ends of helices, but your idea does work! Reassigning the last  
residue of each helix as strand instead displays it as an arrow.

You can control the arrow width in the Ribbon Style Editor (under  
Tools... Depiction).

Ways to reassign secondary structure arbitrarily:

(A) you could select the residues and then in the Selection Inspector  
(opened by clicking the button on the lower right corner of the  
Chimera window), go to the Residue section and set "in helix" to  
"false" and "in strand" to "true."  There are also multiple ways to  
select the residues in the first place.  Without knowing the numbers,  
you could pick from the screen or select from the Sequence panel  
(under Tools... Structure Analysis).  Or you could look up the  
numbers and select them all in a command:

select :12,35,41

However, if you are looking up the numbers anyway you might as well  
just do everything with commands (option (B) below) and not bother  
going through selections.

(B) I think the command way is easier; you just have to look up the  
command syntax.  To reassign residues :12,35,41 in all chains from  
helix to strand:

setattr r isHelix false :12,35,41
setattr r isStrand true :12,35,41

You could also specify chains as needed, e.g. ":12.a,35.a,41.b"
The "setattr" command sets values of existing or new attributes.   
"isHelix" and "isStrand" are existing attributes of residues.  More  
info:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html