[Chimera-users] making microtubule+motor models

[Tom Goddard]

Hi Cynthia,

  The description of making a microtubule model in an earlier Chimera post

	http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-October/011646.html

was just applied helical symmetry to a tubulin dimer.  It is a made-up model not based on fitting actual data.  To do it right start with a microtubule electron microscopy map.  Fit your tubulin, or kinesin or other motor atomic model into the map.  Find the map symmetry (helical pitch, center, axis direction) and apply that symmetry to the atomic model.  You might be able to get the map symmetry parameters with the Chimera "measure symmetry" command

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry

Here is a tutorial making a ParM helical filament model.

	http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/parm.html <http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/parm.html>

Send questions to chimera-users so others will be able to find the answers in the future.

	Tom


> On Apr 16, 2020, at 10:06 AM, Cynthia Page wrote:
> 
> Hi Tom,
> 
> I have found your Chimera user group entry: How to make a microtubule model pretty helpful, thanks for posting this. I am especially naive with Chimera and would like to ask you assistance in making decorated microtubule models as reference maps or cryoem analysis. I can post our conversation to the Chimera group if you think it would be useful.
> 
> I would like to make reference maps for The MiRP/Moors Lab procedure. MiRP interfaces with Relion to perform “helical" reconstruction of molecules bound to microtubules from cryo-em data.
> 
> I have been playing around with you command 
> 
> sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5
> 
> 
> While as you know it works fine with PBD ID 1jff, I cannot figure out how to get results from other PBD ID’s, those with Kinesin molecule and alpha/beta tubulin.  I think the key is "axis x center 0,115,0” portion of this command, and the orientation of molecule as download from the PDB, but for the life of me I cannot figure out how to change the axis coordinates to orient the alph/beta/kinesin correctly. Can you tell me how to do this? I have been using PDB ID’s 3J8Y, and 2P4N.
> 
> Thank you in advance for your time,
> 
> Cynthia Page
> Research Assistant
> University of Colorado, Boulder
> 
> 

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