The process is backtracked to the previous round of automatic grouping. If a round would give fewer than minreg regions (default 1), (default N= 4) and how much smoothing to perform at each round – whether to group by smoothing right after watershed segmentationĪnd if so, how many rounds of automatic smoothing and grouping to perform These apply only to the initial segmentation, not after smoothing. Mincontact contact voxels (default 0) with other regions. – throw out regions containing fewer than minsize voxels If response time after segmentation is slow, tryĭecreasing maxreg and/or increasing triangle-size. Of 1 gives triangles comparable in size to the map grid spacing.Ī value of 2 will make the triangles twice as large (quadruple the area)Īnd reduce their number by about a factor of 4. Smaller surface triangles give a smoother appearance,īut more triangles take longer to render. Subsequent smoothing and grouping calculations. Those which are not displayed will still be included in If more regions than maxreg are generated, however, To maxreg (default 60 largest) and set surface They can also be saved separately using the Segment Map File menu. Segmentation results are included in saved
Segmentation region selection, showing/hiding,Īnd other manipulations can also be performed with the Group will combine the selected regions into a single group. Group traverses the stages in the opposite direction as Ungroup, Ungroup will backtrack to the previous stage of grouping for Segment automatically applies multiple rounds of smoothingĪnd grouping, so that different intermediate stages can be accessedīy clicking Ungroup multiple times. If no segmentation regions are selected,Ĭlicking Ungroup backtracks to the previous stage of grouping of the.Without erasing the pre-existing selection. Grouping and ungrouping can be specified interactivelyĬtrl-click selects a region and Shift-Ctrl-click selects additional regions However, multiple segmentation models can be open at the same time,Īnd may have been generated from different density maps or opened from The current segmentation model rather than creating a new one. Grouping and ungrouping operations modify The Current segmentation is indicated in the dialog and can be changedīy choosing a different segmentation name from the pulldown menu.ĭesignating a segmentation as the current segmentation The segmentation is given the same name as the corresponding map except The resulting number of regions is reported in the The segmentation result is shown as a surface model Smoothing and grouping as specified in the
MAKEMKV SEGMENT MAP APOCALYPSE NOW PLUS
(contour level) of the map should be adjustedīefore segmentation, because the calculation will use only the voxelsĬlicking Segment partitions the chosen map by the watershed method plus The map of interest should be chosen from the pulldown menu of open If interactive rotation speed is poor after segmentation, seeįrom the Volume Data section of the Tools menu So binning should aim for a grid spacing of approximately twice the Gaussian filtering reduces resolution to about six times the GaussianĪfter smoothing, it will also improve performance to reduce the sizeįor visualization and analysis, it is desirableįor a density map to be oversampled by three times in each dimension, Gaussian smoothing to reduce the number of local maxima It may be necessary to process a density map beforehandįor the segmentation to finish in a reasonable amount of time.Ī map of size 256 3 can have a million local maxima if it is noisy.
interactive grouping using fitted atomic models.
MAKEMKV SEGMENT MAP APOCALYPSE NOW MANUAL
interactive grouping by manual selection.However, smoothing the data before segmentation Segger provides various ways to combine regions after the initial segmentation: Often gives more numerous and smaller regions than desired, One region per protein or domain, but the initial segmentation
Own region, and the boundaries between regions lie at the Segment Map performs watershed segmentation:Ī density map is partitioned so that each local maximum has its Segmentation regions can be measured with Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC.Ĭomparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps. Scale-space filtering, and fitting of structures by alignment to regions. Quantitative analysis of cryo-EM density map segmentation by watershed and