[Chimera-users] How to make a microtubule model

Tom Goddard goddard at sonic.net
Thu Oct 22 11:49:16 PDT 2015

  The following page shows a “bent microtubule” model made with a Chimera Python script

	https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html <https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html>

The bend makes it more complicated than a straight microtubule.  Here is an explanation of how the Chimera “sym” command can make a straight microtubule model.

  These commands in Chimera (menu Favorites / Command-line to enter commands) make a straight microtubule from a PDB model as shown in the attached image.

	open 1jff
	sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5

The sym command took the tubulin dimer (shown in red and blue in the image) and made copies in a helical pattern to look like a microtuble.  The trick is to find the right helical parameters.  I just did a few minutes trial and error to find the above.  The “group” option says make a helix where each subunit is shifted 9.8 Angstroms from the previous one and by 27.7 degrees around the axis from the previous one, and make 13 copies (for a 13 protofilament microtubule).  This makes a single turn of the microtubule.  A microtubule does not have helical symmetry, the one turn achieves a shift of 1.5 subunits creating a seam where alpha and beta tubulin are touching in two adjacent protofilaments.  So I just make one turn.  Then the above command says shift that one turn by 80 Angstroms along the axis for each of 8 copies.  The “surf true” option says show the copies as surfaces.  Without that it will copy the atomic model and use a ton of memory.  The helix axis is x (just judged by eye after opening tubulin dimer 1jff.  The 1jff dimer seems to be centered not far from 0,0,0 so I shifted the helix axis 115 Angstroms along y to make the diameter about 23 nm.  Here are the docs for the sym command:

	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html>

  Here’s a web page where I did something more sensible to get better symmetry parameters — I fit the tubulin dimer to an EM map of a microtubule.

	http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html <http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html>


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