XMIPP introductory demo

Figure 19: Chimera visualization of the Random Concial Tilt output mapMask types menu allows to change the shape of the mask. We recommend a circularcrown mask that encapsulates the particle. Then just quit the program using the Quitoption in the pop-up menu and the protocol will continue automatically.2. Compute a kerdenSOMAs described in more detail in section 2.6, the output of the algorithm (see Fig. 21) is a collectionof images (code vectors), which represent the main features of variability in our sample. You canselected code vectors by double clicking the left-mouse button or by pressing the space bar. Youcan save selfiles with images belonging to the selected codevectors by clicking with the rightmouse button in the window. Select File->Save assigned images in a selfileand save the file wherever you want with the browser. Select Options in the same menu tocalculate the average image and standard deviation of the images assigned to the selected codevectors.The relevant question to answer with this SOM is: “is there any remaining structural variability?”.2.10 Want more?We have followed a particular data processing work flow that was suitable for the particular casein this demo (RCT data of a molecule that always falls in the same orientation on the grid andthat shows differences in rotational symmetry that may be used for its classification). If you30