6. Import Input data

Taking advantage of Scipion software framework, we are going to import the above indicated input data using protocols import volumes and import sequence. Details about the parameters of these two protocols are shown in Appendices Import volumes and Import sequence, respectively.

*Scipion* framework with import workflow.

Fig. 6.1 Scipion framework with import workflow.


In the following we will use the notation Fig. X (a) to refer to the figure number X and there will be an arrow labeled with “a” pointing to the region of interest.

6.1. Volume

First open the import volumes protocol (Fig. 6.2 (1)), fill in the form and execute it (2), and finally you may visualize the volume (3).

As you can see, when we import a map we directly assign its sampling rate and its origin of coordinates. If for any reason we have to work with other maps previously generated during the reconstruction process that do not have the desired sampling and origin, we can use the auxiliar protocol assign orig & sampling, detailed in Appendix Assign origin and sampling, to assign them.

Importing the volume in *Scipion*.

Fig. 6.2 Importing the volume in Scipion.

ChimeraX [Goddard et al., 2018] is used for visualization by default . Clicking in the viewer menu (Fig. 6.3 (1)), shows the 3D map and the x (red), y (yellow) and z (blue) axes.

Volume visualized with *ChimeraX*.

Fig. 6.3 Volume visualized with ChimeraX.

6.2. Sequences

The sequences of Hgb \alpha and \beta subunits will be independently downloaded from UniprotKB. First of all, open the form of import sequence protocol (Fig. 6.4 (1)), then complete the form to download HBA_HUMAN protein with UniprotKB accession code P69905, execute the process (2), and finally visualize the sequence (3) in a text editor. The sequence will appear in fasta format as it has been written above. Follow the same protocol to download HBB_HUMAN with accession code P68871.

Importing a *UniprotKB* sequence in *Scipion*.

Fig. 6.4 Importing a sequence in Scipion.