| -create 20,60,30 | Create a new mask of this size in place of input image |
| or using the micrograph orientations in the parameter file. | |
| -find wedge | Find the missing regions and create a new mask. |
| -wedge 45,-70,65 | Missing wedge mask: tilt axis angle, first and last tilt angles. |
| -pyramid | 40,-60,60,130,-55,60 Missing pyramid mask: 2 sets of tilt axis angle, first and last tilt angles. |
| -cone 65 | Missing cone mask: one tilt angle. |
| -invert | Invert mask just before writing the image. |
| -dilate 2 | Dilate mask a number of times. |
| -verbose 1 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -origin 110,50,44 | Origin for the mask (default 0,0,0). |
| -wrap | Flag to wrap around image boundaries (default not). |
| -resolution 20 | Resolution limit (angstrom, default Nyquist). |
| -scale 1.2 | Scale or magnification of mask compared to original images (default 1). |
| 1. Creating a new mask: | |
| bmissing -v 7 -create 100,100,50 -wedge 45,-60,65 -origin 50,50,25 mask.mrc | |
| 2. Generating a mask from an image: | |
| bmissing -v 7 -pyramid 30,-30,70,120,-60,50 -wrap input.map mask.mrc | |
| 3. Generating a mask from micrograph orientations: | |
| bmissing -v 7 -create 100,100,50 -wrap mg.star mask.pif | |