## Masks excluding missing data regions in maps

In tomography the typical limited ranges of tilt angles achievable leaves significant regions in Fourier space unsampled. To compensate for this "missing data" in cross-correlation algorithms, a mask needs to be generated. The different geometries for acquiring tomographic data is reflected in the different ways in which these masks can be generated with the program bmissing.

The examples below have been generated to center the masks in the middle of the volumes. However, the standard Fourier transform (to which the masks will be applied) has an origin at the {0,0,0} voxel. Therefore, to create a suitable mask, the -origin option should be omitted and the -wrap option used.

## Missing wedge mask

A missing wedge is defined by the tilt axis angle (starting from the x-axis and increasing counter-clockwise), and the negative and positive tilt angle extremes.

bmissing -v 7 -create 200,200,200 -origin 100,100,100 -sam 2.5 -wedge 90,-60,60 mis_wedge1.mrc

The missing wedge can also be resolution limited to eliminate higher resolution data that my be dominated by noise.

bmissing -v 7 -create 200,200,200 -origin 100,100,100 -sam 2.5 -wedge 30,-60,60 -resol 10 mis_wedge3.mrc

## Missing pyramid mask

The missing pyramid is just an intersection of two wedges, and requires the specification of two tilt axes and four tilt angles.

bmissing -v 7 -create 200,200,200 -samp 1.34 -resol 5 -pyramid 30,-30,70,120,-60,50 -origin 100,100,100 mis_pyr1.mrc

## Missing cone

A missing cone in tomography is usually the result of rotating a specimen tilted at a constant angle, and only this angle need to be specified.

bmissing -v 7 -create 200,200,200 -samp 1.5 -resol 6 -cone 60 -origin 100,100,100 mis_cone1.mrc

## A missing data mask from an aligned tilt series

The alignment information from a tomographic tilt series can be used to generate a corresponding missing data mask. The mask will then not only repesent the alrge missing wedge at the top and bottom, but also all the small missing regions between the central section planes derived from the images in the tilt series.

bmissing -v 7 -create 200,200,200 -origin 100,100,100 -wrap -resol 20 ccv_060126_1_ref7.star tomo_mask.mrc

To generate a mask with the correct origin, omit the -origin option. The following image also show the small regions of missing data.

bmissing -v 7 -create 200,200,200 -wrap -resol 20 ccv_060126_1_ref7.star tomo_mask1.mrc