[chimerax-users] Applying symmetry operations to generate an oligomeric model

[Tom Goddard]

Hi Rob,

  It sounds like you did everything right.  Using "measure center #1" where model #1 is the map should give the right center of the tetrahedron.  When you use that command it reports the center in map grid index units and also in scene coordinates, for example,

measure center #1 <cxcmd:measure center #1>Center of mass grid index for emdb 15560 = (279.52, 279.92, 253.25)
Center of mass xyz coordinates for emdb 15560 = (289.20, 235.85, 185.32)


In the sym command were you use that center to copy your atomic model with tetrahedral symmetry you should use the scene coordinates (the second line of output) not the grid index coordinates.  The "sym" command expects scene coordinates for the "center" option and you should not use the "sym" command coordinateSystem option.   The coordinateSystem option is used only if the center coordinates are given in the coordinate system of a specific model rather than the whole scene.  The models start out with the same coordinate system as the whole scene, but if you move a model in the scene (e.g. when you fit an atomic model into the map) then that model has different local coordinates than the scene.

  I see another potential problem in your sym command.  The "axis" option is supposed to be a 3-fold symmetry axis of the tetrahedron.  You are giving it the symmetry axis of the asymmetric unit trimer which may or may not be a symmetry axis of the tetrahedron.  To determine the symmetry axis of the tetrahedron open two copies of the map and rotate one copy by hand using the "Move Model" mouse mode (which moves only the selected model) to roughly align two different trimeric subunits then optimize the alignment with "fitmap #2 in #1", then use measure rotation #2 to #1 and it will report a symmetry axis of the tetrahedron.  Another way to go about this is if you density map already has a standard orientation, such as tetrahedron 2-fold symmetry axes along x,y,z then you don't need to specify the axis in the sym command, just use "t,222" in the sym command.  Or if it has a symmetry axis along z use "t,z3" with no axis specification.  You can probably see if it has a standard symmetry using "measure symmetry #1".

  Sorry for the delayed answer.  I was at a workshop all last week and did not have time for email.

	Tom

> On Nov 3, 2022, at 4:35 AM, Robert Harkness via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> I am trying to generate a model of an oligomeric protein cage that consists of 4 trimers and has tetrahedral symmetry. I am using the asymmetric unit model consisting of one monomer (#0) and a density map (#1) as a starting point. My strategy has been to take the asymmetric unit and fit it into a portion of the map corresponding to one of the monomers within one of the trimer faces of the tetrahedron. Then I generate a copy of that asymmetric unit (#2) and fit it into the map for an adjacent protomer within the same trimer face. This results in the two asymmetric unit models being rotated 120 degrees relative to one another and part of the same trimer. Then I use the measure rotation command to measure the rotation of the second asymmetric unit relative to the first, giving me a rotation matrix and axis parameters. I then do
> 
> sym #0 (first asymmetric unit) group t,z3 axis <axis from measure rotation> center <axis points from measure rotation> coordinateSystem #1 (the density map)
> 
> And this generates the right looking trimers, so the 3-fold axis appears to be correct, but the center is off such that only one of the four trimers matches the density map and is placed at the top of the tetrahedron, while the other 3 trimers are off into the void of the scene but placed at the other 3 vertices. I am not sure how to appropriately define the center. My feeling is that it should be the center of the map, taken from the measure center #1 command, but implementing those numbers in sym doesn’t work either. Any thoughts on how these center coordinates are defined/should be measured, or if there is a better approach for doing this would be awesome!
> 
> Best,
> 
> Rob
> 
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