mrc files written have incorrect space group in the header

[attamatti]

I've found that the maps, masks, and halfmaps written by Relion (At least as of the Relion 5..0 tutorial data) have the space group in the mrc header set to 0 for 3D volumes it should be 1.

[biochem-fan]

Thank you very much for pointing this out. Your point is correct.

I will see if this can be fixed. This might be non-trivial because RELION's routine does not really distinguish a 3D volume and a stack of 2D images.

[colinpalmer]

Just to add, RELION does seem to maintain a consistent difference between a 3D volume and a stack of 2D images in other respects:

• 3D volumes are always given a .mrc extension while 2D image stacks have .mrcs
• 3D volumes have the header's MZ value set equal to NZ while 2D image stacks have MZ set to 1

So I'd hope it might be possible to find the place(s) where those things are set and adjust the space group value at the same time.

[biochem-fan]

@colinpalmer That is a great pointer.

Can you (@colinpalmer or @attamatti) test the following patch?

diff --git a/src/rwMRC.h b/src/rwMRC.h
index 03f34c70..8ed19b04 100644
--- a/src/rwMRC.h
+++ b/src/rwMRC.h
@@ -330,9 +330,15 @@ int writeMRC(long int img_select, bool isStack=false, const int mode=WRITE_OVERW
        header->nx = Xdim;
        header->ny = Ydim;
        if (isStack)
+       {
                header->nz = Ndim;
+               header->ispg = 0;
+       }
        else
+       {
                header->nz = Zdim;
+               header->ispg = 1;
+       }

        // Convert T to datatype
        DataType output_type;

[biochem-fan]

@colinpalmer or @attamatti
If you could confirm the above patch fix the problem, I would merge this patch to the code base.