[chimerax-users] align 400 copies of the same density map into a circle

[Tom Goddard]

Hi Shiqing,

  The ChimeraX sym command can show copies of an atomic model rotated about some center, for instance,

	open 1a0m
	sym #1 C400 center 500,0,0

shows 400 copies of this atomic model rotated about the z axis.  It does not make 400 copies, it just shows the one copy in 400 positions which takes much less memory.  You could add a "copies true" option if you really wanted to make 400 copies and have enough computer memory to do it.

  The sym command does not work on maps.  I am not sure why it doesn't.  But you can copy the positions of the atomic model to the map.  For example,

	open 1a0m
	molmap #1 5
	sym #1 C400 center 500,0,0
	view position #2 sameAs #1

You will need a May 17 ChimeraX daily build or newer for this to work because the "view position" command was not handling multiple copies so I fixed it just now.  Again this just tells ChimeraX to display the map at 400 positions and does not make copies of the map.

  Here is the documentation for sym and view position:

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html#position

  Tom


> On May 12, 2022, at 6:56 PM, SHIQING LIAO via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi there, 
> 
> I am a new user and would really appreciate any input on the task I want to do using Chimerax. 
> 
> Currently I have a mrc map, and it is a part of a cylindrical tube-shaped structure (like the area I drew in the picture). The map looks like a curved plane from the side of the cylinder, if it helps. If I piece 400 identical copies of map with some rotation and transition, I would ideally get a cynlider shaped strutcure, without top and bottom (like the picture below). 
> 
> The reason why I want to piece the mrc together is that I don't have the full look of the tube, but I know the rough radius (that's how 400 was derived), and I want to make a model for the full tube, using the model of the composing protein. I managed to manually fit the models of individual protein into one map. For the other mrc copies, I tried to do the same again but it took a lot of time and not very accurate, so I'm looking for any coding solutions that might help.  
> 
> I'm currently thinking if it is possible for me to place a marker at the center of one mrc map. Then make 400 copies of the map with the marker. Then write a code to tell each 1/400 mrc map to rotate 0.9 degrees around the marked center and move to a coordinate. Then I can repeat the same for the protein models I mapped to one mrc map. But I have no idea how to achieve it, and any suggestions would be greatly appreciated! Thank you so much for helping me!!!
> 
> Best,
> Shiqing
> 
> <cf23fde5-632f-4568-9700-9307f24e0f6c.png>
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