XMIPP introductory demo

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Figure 4: Output visualization of Xmipp Preprocessing Micrographs protocol. The all_ctfs.selwindow shows the CTF of all the micrographs. In this case is shown the CTFs of atilting pair. The first one is very poor defined and ellipse-shaped because it correspondsto the tilted images, whereas the second one is the CTF of the untilted micrograph.Figure 5: CTF of good, astigmatic and drift micrographs12
pair2_untilted/down3_pair2_untilted.raw pair2_tilted/down3_pair2_tilted.raw 1Where the first column contains the untilted image and the second column the tilted imageof each pair. The third column contains a normal selfile-like flag. Now, create your ownall_pairs.sel in the Preprocessing/ folder using you favorite text editor. For example,type:nedit all_pairs.sel &2.3 Manual Particle SelectionClose the Preprocessing GUI, go back to the main menu and click in the Manual ParticleSelection button. This will launch a window as shown in Fig. 6. Introduce the name ofthe micrograph selfile (in this case all_pairs.sel), and indicate that your micrographs aretilt pairs. Then, press Save & Execute, and a window as shown in Fig. 7 will appear.Click on Mark! to select particles in each pair of micrographs. This will launch an overviewwindow containing both micrographs and two zoom windows, one showing part of the untiltedmicrographs and the other showing part of the tilted micrograph (see Fig. 8).In order to select particles:• Arrange the zoom windows, such that the untilted micrograph is on the left side of yourscreen and the tilted one is on the right side. Perhaps you may want to enlarge the sizeof the zoom windows and make the overview window smaller (depending on the size ofyour screen). Just drag the window’s corners to do so.• Click with the mouse left button on the overview window for selecting the part of themicrograph in which you are interested (it will appear magnified in the respective zoomwindows). Use Ctrl+ and Ctrl- in the overview window to Zoom-in and Zoom-outrespectively.• Mark particles with the left mouse button in the zoom windows: First select a particlein the untilted image. This will suggest a corresponding point in the tilted micrograph.You may move its position by clicking the left mouse button on the desired position in thetilted image. You have now selected your first pair.• Initially the suggestions will be far off, but if you have correctly identified several pairs,they should improve. To explicitly recompute the transformation matrix select File->Saveangles (it is a good idea to do first File->Save coords, just in case something goeswrong). IMPORTANT: click a few pairs (at least four) before computing the transformationmatrix. Note that once the correct transformation has been found, the program shouldaccurately predict the position of the tilted particle after identifying the untilted one. Ifthis is not the case, you have probably included some incorrect pairs.• Click with the mouse right button over a selected particle in order to remove it or move it.13
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: Figure 3: Xmipp Preprocessing Micro
Page 15 and 16: Figure 7: GUI for Xmipp Manual Part
Page 17 and 18: Figure 10: GUI of xmipp_protocol_pr
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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