[Chimera-users] curved helices - cylinder representation?

Tom Goddard goddard at sonic.net
Wed Aug 12 12:06:26 PDT 2015


Hi Oliver,

  You have so many ideas it will great to get you to start programming Chimera so we can retire!  Here is example helix tube Python code.  When you open this file in Chimera it will register a new command htube that moves helix CA atoms to the average position over a sliding window.  Here’s an example using the command (image attached):

	open 3ch3
	htube #0 windowSize 6 radius 1.5

You can omit the windowSize and radius options.

	Tom

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> On Aug 11, 2015, at 2:50 PM, Oliver Clarke  wrote:
> 
> 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.
> 
> <Screenshot 2015-08-11 17.30.56.png><Screenshot 2015-08-11 17.33.26.png><Screenshot 2015-08-11 17.33.26(2).png>
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