[Chimera-users] Fitting the structure into the map after changing origin

Tom Goddard goddard at sonic.net
Mon Jul 22 11:08:37 PDT 2019

Hi Ahmad, Elaine,

  The matrixcopy command will not realign a model with a map after the map origin.  The map origin (set by volume viewer panel  menu Features / Coordinates) adjust the coordinate system of the map to set where x,y,z = 0,0,0 is in the 3d map array.  It does not change the matrix that positions the map.  If you fit an atomic model to a map you should set the origin for the map that you want before fitting.  There isn't a simple way to move a fit model after you change the map origin.  But there are not-so-simple ways, for example, if you changed the map origin by 50 grid points in x, and the voxel size was 3 Angstroms, then you moved in 150 Angstroms and you can use the "move" command with the models option to move the atomic model by 150 Angstroms

	move 150,0,0 model #2


> On Jul 22, 2019, at 9:24 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ahmad,
> If the model was already saved/reopened in the original fit position (fit to the previous position of the map), then you could try using command “matrixcopy” to make it follow the map.  However, if you had not saved it in the original fit position, that would not work. 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>
> E.g. if when you open the atomic model it is in the “old” fit position, and it is #4 and the moved map is #2, then you could try
> matrixcopy 2 4
> …but if that doesn’t work you probably just need to start over and re-fit the atomic model to the new map position.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jul 22, 2019, at 7:31 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
>> Is there a shortcut way of transforming the model to fit the map after I change, center or reset the origin? 
>> Best regards. 
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