15. Summary of results and submission
15.1. Submission to public databases
Although submission of cryoEM maps and derived atomic structures to databases has to be done by direct online request (wwPDB OneDep System), Scipion may contribute to organize the submission records. The protocol export to DB allows to perform this task (Appendix Submission to wwPDB). By using this protocol we can save the files that you have/want to submit to databases in a labelled folder and in the appropriate format for submission. Fig. 15.1 details the protocols of the modeling workflow involved in this task.
When you submit the map and the model of a cryo-EM experiment, besides these two records, an image of the map is also mandatory to submit. Other maps, such as half maps or postprocessing-sharpening maps, as well as maks, are also recommended to submit. In addition, the FSC file is strongly encouraged. As you can see in Fig. 15.1, we can provide directly from the workflow the map and the model, as well as the two sharpening maps. The map image can be attached from a file. We lack, however, from the FSC file, since the FSC file is usually generated during the map reconstruction process starting from the half maps, for example with the xmipp3-resolution 3D protocol (Fig. 15.1, red arrow). To compute the FSC file we could download the half maps from the database (PDBe EMD-3488) selecting the zip Bundle (Fig. 15.2 (red arrow)).
The zip folder contains the FSC file (emd_3488_fsc.xml) and the map image (emd_3488.png) but, unfortunately, lacks of half maps. Then, you can use any two half maps and compute the FSC file, just to submit it with the rest of the files.
To save all the relevant files in a single labelled folder, open the export to DB protocol (Fig. 15.3 (1)), and complete the form with the Scipion elements to export: Main map (2), Additional maps: “Yes” (3), the two sharpened maps as additional maps (4), the FSC file if you count on it (5), Atomic structure (6) and Image (7), previously saved in a known folder. Then, write the name of the exportation directory path, or find it with the browser on the right. All submission files will be saved in the directory selected (8). A directory name related with the submission (number, date, project,…) is recommended.
After executing the protocol (9), you can check that all files are saved in the given directory. No additional visualization tools have been included in this protocol.
15.2. Publication of results
select #2/A,B save /tmp/chainAB.cif format mmcif models #2 selectedOnly true open /tmp/chainAB.cif scipionwrite #3 chainAB_ exit
CASE A:Contacts between any couple of members of the whole macromolecule (Fig. 15.4 (3)):This option allows to get all contacts between all couples of members of the macromolecule. In the case of the human metHgb we have depicted all those possible contacts in Fig. 15.5 (A).
The protocol chimerax-contacts can be used to obtain the contacts depicted. Open this protocol (Fig. 15.6 (1)) and fill in the first Input (2) in which no symmetry will be applied. Include the docked 5NI1 structure (4) as Atomic structure. Use the wizard on the right to label the molecule chains (5) as they appear in the adjacent window, and execute the protocol.
The viewer window of the protocol ChimeraX contacts display different results (Fig. 15.7 (A)):
- 3D Visualization box: Final atomic structure considered to compute contacts that can be visualized with ChimeraX. Press the eye (1) to open the structure shown on the right.
- Interacting chains box: Summary list of all interacting chains, similar to the list shown on the right of the Fig. 15.5 (A). Press the eye to open it (2).
- Contacts between interacting chains box: In addition to the possibility of changing the order of the interacting chains in the display, as well as the maximal distance between residues to group them, this box allows to select couples of interacting chains (4) and inspect in detail the contacts between them pressing the eye on the right (3).
CASE B:Contacts between any couple of members of the asymmetric unit and ”non-redundant“ contacts between one member of the asymmetric unit and another one from the neighbor asymmetric unit (Fig. 15.4 (5)). This second asymmetric unit has been obtained by applying symmetry with the protocol chimerax-contacts. Then, “non-redundant” interaction means any interaction that can not be inferred by symmetry. The Fig. 15.5 (B) shows the total number of interactions of our example. The interactions between the chain B of the asymmetric unit (model #1.1) and the chain A of the neighbor asymmetric unit (model #1.2) are symmetric to the interactions between chain A of the asymmetric unit (model #1.1) and chain B of the neighbor asymmetric unit (model #1.2). Since those interactions can thus be inferred by symmetry, they are “redundant” and are absent of the final list of contacts.Similarly to the case A, the protocol form has to be open (Fig. 15.6 (1) ) and completed as indicated in the second Input (3). Include the asymmetric unit structure saved with the protocol ChimeraX operate (6), use the wizard on the right (7) to label the chains as it is shown on the right and, finally, include the respective type of symmetry of the human metHgb (8).Like in the case A, after executing the protocol all non-redundant atom contacts between any couple of proteins indicated in Fig. 15.5 (B) can be visualized by clicking Analyze Results (Fig. 15.7 (B)). Besides the lower number of contacts displayed, remark that a relevant difference between the results of the case A and the case B is the final atomic structure visualized with ChimeraX, which discriminates between the starting asymmetric unit and the second one generated by symmetry.
NOTE:This second possibility of getting protein contacts observed in the case B is extremely useful when you have a big asymmetric unit, for example of a virus, and you are interested in contacts among proteins within the asymmetric unit and with other adjacent asymmetric units.