[chimerax-users] Center of cube in mrc

[Tom Goddard]

Hi Luis,

  MRC files define an origin in the binary file header.  Sometimes that origin is the center of the box, sometimes the lower left corner, sometimes in different position.  ChimeraX uses the center defined within the MRC file.  If you open the file in ChimeraX then you can see the origin used with menu Tools / Volume Data / Map Coordinates.  The "Origin index" indicates the grid index where x,y,z = 0,0,0 (Angstrom units usually).  In the example below it lists the index as 0 (which is shorthand for 0,0,0 since it is the index in 3 dimensions), meaning for this MRC file the origin was the lower left corner of the file.  The origin index could be changed with a ChimeraX command, e.g. "volume #1 originIndex 191.5,191.5,191.5" to move x,y,z = 0,0,0 to the center of the box where this map has 384 by 384 by 384 grid points.  All ChimeraX commands like moving a model with the move command use physical coordinates (Angstroms), not grid indices.

	Tom 



> On Aug 20, 2020, at 10:41 AM, Luis José Castillo Valverde <luis.castillo.valverde.98 at gmail.com> wrote:
> 
> Hello, 
> 
> I want to move a mrc near another mrc from terminal controlled, the problem is that I don't know how ChimeraX defines the center point of movement when loading a mrc file. So I wanted to know if you can explain to me that ChimeraX defines the X, Y, Z coordinates in which it will load the center of the cube?
>  
> Best regards,
> 
> 
> Luis
> -- 
> 
> Luis José Castillo Valverde
> Ingeniero en Computación, TEC Costa Rica
> Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica
> Telegram: @LCastillo98
> LinkedIn: luisjosecastillo98
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