XMIPP introductory demo

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Figure 16: output ML2D classification GUI. This visualization protocol show the results ofml_align2d protocol.26
Press Show Expert Options and in Additional WBP Parameteres write -symc6. Then Press Save & Execute.The protocol consists of several steps:1. Prepare all images of the selected class(es), apply the alignment information in the headersof the untilted images to the headers of the tilted images and precenter the latter ones.2. Perform a 3D reconstruction with the centered tilted images. This option can be performedusing the faster option WBP or the potentially more accurate option ART.3. Low-pass filter the reconstructed volume(s).When the protocol finishes you can visualize its results by pressing the Analyse Resultsbutton. This GUI offers several options for visualization (see Fig. 18). You can check theuntilted aligned images, the average of this images and the different 3D reconstruction. In theupper part of the GUI you can select which of the maps you want to visualize, whereas in thelower part you must select the way in which you want to visualize them. You can visualize themap by slices along the three different axis (X,Y and Z) or by surface rendering in case you haveUCSF Chimera installed in your machine (see Fig. 19).NOTE: In order to speed up the different steps involved in this <strong>demo</strong> we have masked verytightly the experimental data. In fact, they are saved as 50x50 pixels images instead of the80x80 pixels images used by Núñez-Ramírez et al. (2006). The side effect of this policy is theappearance of artifacts at the volume borders.2.9 KerdenSOM ClassificationNow we will make a little excursion to have a more detailed look at the KerdenSOM algorithm.We will use it to look for additional heterogeneity inside the other class of G40P (simC3.sel).First, you will again need to align the images of this selfile, otherwise the main heterogeneitythat you would find would be in shift and rotation of the images. To align the images you canagain use the ML2D classification protocol (following the instructions as given in section 2.7).Once the images are aligned, press the KerdenSOM classification button in the mainmenu, and fill out the form as shown in Fig. 20. Introduce correctly the directory where youhave perform the alignment by xmipp_ml_align2d, and indicate which class of this run you wantto use (in this case there is only one class!).The protocol comprises two steps:1. Design a mask that defines the region of interest in the average image of all particles. Thisprocess is user-interactive and will launch a graphical tool that will allow you to designmasks of different shape or size. Play with this tool until you have a suitable mask forthese data. Click the right mouse button in the window to pop-up a menu. In the Help->Help! you will find instruction on how to change the size and position of your mask. The27
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 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: Figure 15: ML2D classification GUI2
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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