[Chimera-users] curved helices - cylinder representation?

[Oliver Clarke]

Hi all,

I’d like to have an extended version of the “Pipes and planks” representation, where helices are represented as cylinders, except as a regular, easily modifiable ribbon representation, and allowing for helix curvature rather than breaking up curved helices. I realize this is not currently implemented and is unlikely to be addressed until Chimera 2.0 due to the many other more important things on the drawing board, so I’m trying to figure out a way to hack something together that will generate acceptable results in the meantime. 

I figure that one way to do this might be to use a create a pdb file with guide atoms located on the helix axis, which one can approximate by placing a guide atom (P or CA) at the center of mass of a six residue sliding window of C-alpha atoms, and then use these guide atoms to create a thick, smoothed (with B-spline) licorice tube. 

This works quite well for an individual helix, as you can see in the attached pics, but I am a little at a loss as to how to automate this procedure across all the helices in a structure, or even for a given (selected) helix (and it’s only really the helices I care about - strands are fine as is, but having a curved cylinder representation for helices would be very handy). I guess I can do so using a python script of some sort, but if anyone has any pointers as to how to get started, they would be most appreciated.

So I guess I need to loop through all the residues in a selection, calculating the center of mass in a sliding window and placing atoms as appropriate, then write out a pdb file with appropriate atom names. This shouldn’t be too hard, but if anyone can point me towards code that I can adapt for this purpose it would be most helpful.

Cheers,
Oliver.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150811/febc991d/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2015-08-11 17.30.56.png
Type: image/png
Size: 188153 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150811/febc991d/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2015-08-11 17.33.26.png
Type: image/png
Size: 199698 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150811/febc991d/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2015-08-11 17.33.26(2).png
Type: image/png
Size: 200679 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150811/febc991d/attachment-0002.png>