Dear Michele,
If you open maps in Chimera, it could be that the maps are displaced due
to different orign offsets in the header of the MRC files. You can set
these all to zero using the 'coordinates' option in the volume viewer.
Relion will always ignore the header. You can confirm that the mask and
map overlap using the 2D slice-viewer in relion_display.
HTH,
Sjors
> Dear all,
>
> I am doing a focussed refinement with relion 1.4, because my protein
> complex is composed by subunits with different symmetries.
> I followed this procedure:
> - initial map reconstruction without symmetry;
> - segment the map with chimera and segger, and save the map corresponding
> only to the volume of interest;
> - use this map to make a mask with relion_mask_create; I extended the mask
> 3 pixels and used a soft edge of 6 pixels;
> - use this mask for the refinement (--solvent_mask); the corresponding map
> created in chimera/segger is used as reference (--ref);
>
> This procedure worked fine for one half of the complex. The other half
> gave
> me a strage result: when I open the refined reconstruction and the solvent
> mask, the later appears displaced, i.e. is not anymore around the volume
> of
> interest. The refined map shows the strongest features not anymore in my
> volume of interest, but in the volume which appears included in the
> (displaced) mask.
>
> I wonder why is this happening? How are placed the solvent mask and the
> reference in the particle volume?
>
>
> Thank you in advance for any suggestion
>
> Michele
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
|