[Chimera-users] Rotate and transform command

[Elaine Meng]

Hi Dashuai,
This is a frequently asked question… the reason is that map files do not contain rotation information. 

If the map was fitted to another map, the solution would be to resample the rotated map on the grid of the other to create a third map,  see “saving maps after fitting":
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>

if you don’t have another map grid already, one idea is to make new zero-valued map with “vop new” and then resample your rotated map on the grid of that zero-valued map. However, you’d have to create the new map so that it encloses your existing rotated map (show box outlines with Volume Viewer).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 20, 2018, at 8:38 PM, 大帅 <527655229 at qq.com> wrote:
> 
> Hi,
> 
> Therefore, we used UCSF Chimera to have a map's smmetry axes (approximately) parallel to the XYZ axes. The procedure followed by the relion tutorial we used for that was to
> read in InitialModel/symC1/run_it003_class001.mrc; use the duplicate
> option under the File menu of the Volume viewer. Then to deactivate map
> #1 on the Model Panel; rotate map #0 to have it’s symmetry axis more or
> less parallel to the XYZ axes; and then to use in the Command Line entry field:
> run_it003_class001.mrc; and save this model in the InitialModel/symC1/
> directory with the name inimodel.mrc
> 
> I have done as the above tutorial in relion, but the saved inimodel.mrc file does not change its position or  orientation at all. So, my question is what commend can save a map after rotating or transforming its  x,y,z coordinate ? What is the procedures to do so ?
> 
>                                                                                                Thanks
>                                                                                                  Dashuai