Section 25.2.1.10.3. Averaging mask construction

Masks encompassing the region(s) to be averaged are usually created by hand in the interactive program MAPVIEW. Here, one reads in a submap comprising the desired region of whatever type of map is available, usually an MIR map. An appropriate contour level and initial section are selected and the contoured electron density for that section appears on the screen. One then selects the `add next section' menu item two or three times to create a projection over several sections of the map, since in the projection the molecular boundary is usually more obvious. Selecting the `trace mask' menu item then allows the user to hand-contour the molecular envelope by directing the cursor tied to a mouse or other pointing device. One then moves to an adjacent section and repeats the process until the complete 3D mask is obtained. To simplify matters and speed up the process, there are `copy next mask' and `copy previous mask' menu items allowing one to take advantage of the fact that the mask is a slowly changing function, particularly when near the centre of the molecule. One can use this feature to copy a mask from the previous or following section and apply it to the current section. Up to twelve distinct 3D masks can be selected. Each mask is colour-coded and can be simultaneously displayed superimposed on the contoured electron-density section. Once the mask is completed, the `make asu' menu item is selected to apply crystallographic symmetry operations to all points within the generated envelope masks. If these operations generate a point also within the envelope masks, the point is flagged in red to indicate that it is redundant, indicating that when tracing the mask, one inadvertently strayed into a symmetry-related molecule. After this check for redundancy, all points within the submap distinct from but related to points within the molecular envelopes by crystal symmetry are flagged in green. This enables one to detect packing contacts and also to ensure that all significant electron density has been assigned to some envelope. Upon completion, the mask is written to a file suitable for use either in averaging, solvent flattening (after expansion by BLDCEL), or operator refinement. In cases of `proper' NC symmetry, it is often desirable to trace the averaging envelope mask in a `skewed' map, such that one is looking directly down the NC rotation axis. In this case, it is usually very obvious where the NC symmetry breaks down, simplifying identification of the averaging envelope. If the averaging mask is created in a skewed submap, then the batch program TRNMSK can be used to transform it so as to correspond to the original, unskewed submap for use in averaging calculations (which do not require skewing).