[Chimera-users] How to find symmetry parameters for icosahedral molecule

Tom Goddard goddard at sonic.net
Thu Dec 8 11:00:26 PST 2016

Hi David,

  If this is a single-particle reconstruction where icosahedral symmetry was imposed on the map you'll want to apply exactly that symmetry to the molecule.  The two things you need to know are the grid point that is the center of symmetry, and the orientation of the icosahedral axes (e.g. 2-folds along x,y,z, or 5-fold along z, ...).  It is unfortunate that this information is not stored with single particle maps, so you often have to deduce it.  Here's my usual approach.  I use the Chimera Icosahedron Surface tool (menu Tools / Higher-Order Structure) which shows an icosahedron superimposed on your map.  If it is not centered on the map I adjust the map center using the volume viewer dialog menu Features / Coordinates and adjust Origin Index usually to the midpoint of the box (if grid size is 500, I try 250 for the center index, or it could be 249).  I adjust the radius of the icosahedron using the icosahedron tool so it matches the map.  Then I try the different Orientation settings in the icosahedron tool to find the one that matches the icosahedral symmetry of the map (5-folds match with 5-folds, 3-folds match with 3-folds...).  Once you have that and you have a copy of your molecule #1 docked with the map #0 with the map origin set to center of symmetry you can use the sym command to make copies, for example, 

	sym #1 group i,222r center 0,0,0 coordinateSystem #0


> On Dec 8, 2016, at 12:16 AM, Haselbach, David <david.haselbach at mpibpc.mpg.de> wrote:
> Hi everyone, 
> sorry to ask such a basic question. I have a cryo EM density map 3.2 A of a icosahedral molecule and I already build the model of the monomer. I would like to place the remaining 59 copies and calculate the BioMT matrix for it. I started playing around with the sym command, but I couldn’t get it working nicely. It’s probably a problem of the coordinate system, but I couldn’t figure it out. Than I thought there must be an automatic way and I tried Multifit but also this failed me miserably as the runs fail continuously with “stderr”.  So I was wondering is there a protocol to do this?
> Already thank you for any suggestions, 
> David
> Dr. David Haselbach
> Max-Planck-Institute for biophysical Chemistry
> Department for structural Dynamics
> Am Fassberg 11
> 37077 Germany
> Tel. +495512011302
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