Reducing Background of Near-Atomic Resolution Cryo-EM Structures with Fitted Maps for import into Sketchfab
Figure 9. Opening the Zone Feature in UCSF-Chimera
After selecting the Zone tool, new tools appears on the Volume Viewer (e.g, Zone and Mask). Clicking the button labeled “Zone” removes all of the density of the cryo-EM map except that surrounding Chain A (Figure 9).
Step 5. To the right of the Zone button is a button labeled “Mask”. Clicking this button masked the select region of the the cryo-EM density and created a separate density object, which added a corresponding pane in the Volume Viewer window (Figure 10). Similar to the original Volume Viewer, this new window allowed us to adjust the resolution or color of the cryo-EM masked region.
After clicking the “Mask” button, a new list item was also added to the Model viewer, “1 emd_2984.map zone” (Figure 10).
Figure 10. Apply the Mask to The Zone Region in UCSF-Chimera
With we clicked the “Mask” button, the default gray cryo-EM mesh changed color to yellow (Figure 10). Using the color tool for the new created mask, we changed the color from yellow to blue (Figure 11).
Figure 11. Changing the Mask Region Color
Figure 12. Masking Chain B
Step 6. To mask another region of the cryo-EM density map, we followed the same procedure (described in Steps 1 – to 5). For this procedure to work properly, it was very important to UNCHECK the model we just completed (i.e., Chain A). Once Chain B was checked and the “Apply”pushed, it was zoned and masked. As shown in Figure 12, Model B is checked and model A is unchecked. Again the region of the cryo-EM map masked was colored automatically (cyan) and an additional item was added to the Model Panel (i.e., “2 emd_2984.map zone”).
Figure 13. Masking Of All 4 Chains
As mentioned earlier, generating mask of the cryo-EM map adds additional items to the Model Panel list. We examined if these newly generated items could be used in conjunction with API scripts (provide by Mr. James Green and Mr. Corentin Metgy at Sketchfab) to hide and unhide various regions of the CryoEM directly in Sketchfab.
Using the names assigned in the Model Panel directly in the script did not work using the Sketchfab API. However, manual inspection of the output data file indicated subnode_119, subnode_220, subnodes_221 and subnode_222 were regions corresponding to the newly generated zone / mask applied to the cryo-EM mapduring the procedure. This was also confirmed by importing the model into other software and examining the naming convention used for the individual items.
It was possible to script buttons such that individual masked regions of the CryoEM (corresponding to the assignment in UCSF-Chimera) can be hidden or revealed (e.g., clicking on the EMD 2984 button will load the entire CryoEM structure. Clicking on the Zone A button will hide all other zones and reveal only zone A.) (Figure 14).
Figure. 14 Hiding EMD 2984 Zone Mask in Sketchfab
The above Zone/Masking technique was applied to EMD 2984 Volume Viewer settings in the “normal” signal-to-noise viewing range (i.e, step 2, level 0.03). After masking, we could increase the step or surface level settings of the individual zoned regions with no increase in background.
To test if this method would work using increased settings at the beginning of the procedure, the Volume Viewer settings were changed to Step 1 and level 0.015. As seen in Figure 15, these settings generate very high background noise such that the CryoEM structure was obscured. Nevertheless, using the zone/masking procedure described above, a high resolution model was produced (Figure 16).
Figure 15. EMD 2984 with high background levels in Chimera
Figure 16. High Resolution EMD 2984 imported into Sketchfab.
Near-atomic resolutions structures are now being generated by CryoEM. This new technology could soon revolutionize the drug discovery process as well as shed light on complex biological mechanisms and disease processes.
Unlike other CryoEM data, many near-atomic resolution EMD files contain associated fitted molecules. Combined, these CryoEM and PDB files can be extremely large and difficult to manipulate at high Volume Viewer settings.
Whereas most scientist working in the field have access to high-end computers, sharing these fitted-map structures via social media could be problematic.
As shown here, once these zoned and masked structures are imported into Sketchfab, viewing and sharing large near-atomic resolution structures is possible on almost any computer. Viewing on mobile devices is possible, but optimization techniques will have to be addressed for these high polygon count uploads.
Acknowledgments: Mr. James Green and Mr. Corentin Metgy at Sketchfab for providing the initial API Script.
To read more about the UCSF-Chimera Zone / Masking, visit the USCF Chimera site:
Publications describing the UCSF zone algorithm