XMIPP introductory demo

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Figure 9: A field of evenly distributed particles is shown on the left panel. On the right panelsthere are examples of micrographs with too many or heterogeneous particles. Barrepresents 50 nm.facilitate subsequent image processing steps. Some micrographs that were not discarded inthe CTF estimation, may be discarded at this stage, as a too high particle density or a strongheterogeneity in the particle population may hinder the selection process. Some examples aregiven in Fig. 9.By pressing the File->Save coords button in each window, the program saves a positionfile for each micrograph. Pressing File-> Save angles button saves a so-called angle file(with information about the transformation matrix) for each tilt pair. The position files are insidethe corresponding micrograph directory and the angle file is saved inside the correspondinguntilted micrograph directory. You can see them typingls */*.posls */*.angThe angles file looks like:# alpha_u alpha_t gamma75.783 74.6211 55.9613The tilt angle is the third value and should be (for this particular example) about 55º while thefirst two values (alpha_u and alpha_t) are the angles between the tilt axis and the y-axis for theuntilted and tilted image respectively. These values should be, for this particular example, about75º. As you select more and more particles the accuracy of these values should increase. (If youdo not get values close to these ones you have probably selected incorrect pairs.)2.4 Preprocess particlesClose the Manual Particle Selection GUI, and click on the Preprocess particlesbutton of the main menu to continue. This will launch the GUI of the next protocol that will allowyou to extract, normalize and correct the CTF-phase of your picked particles. Modify theparameters of the Preprocess Particle Protocol according to the parameters shownin Fig. 10.16
Figure 10: GUI of xmipp_protocol_preprocess_particles17
Page 3 and 4: 1 General introduction1.1 Welcome t
Page 5 and 6: xmipp_selfile_create "my_experiment
Page 7 and 8: 2 Your first 3D reconstruction in X
Page 9 and 10: Figure 2: Xmipp Protocols main menu
Page 11 and 12: Figure 3: Xmipp Preprocessing Micro
Page 13 and 14: pair2_untilted/down3_pair2_untilted
Page 15: Figure 7: GUI for Xmipp Manual Part
Page 19 and 20: Figure 11: Analyse results window o
Page 21 and 22: Figure 12: xmipp Rotational Spectra
Page 23 and 24: Figure 14: Analyse results window o
Page 25 and 26: Figure 15: ML2D classification GUI2
Page 27 and 28: Press Show Expert Options and in Ad
Page 29 and 30: Figure 18: Output Random Conical Ti
Page 31 and 32: Figure 20: KerdenSOM Classification
Page 33 and 34: would like to continue with these d
Page 35 and 36: Figure 22: Flow chart of possible d

XMIPP introductory demo

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