Reducing Background of Near-Atomic Resolution Cryo-EM Structures with Fitted Maps  for import into Sketchfab

V.F, S.S

Summary:

This tutorial supersedes previous tutorial detailing manual background noise removal.

The following tutorial demonstrates a way to use the zone / masking tools in UCSF-Chimera to directly produce high resolution, low background models from cryo-electron microscopy (cryo-EM) data for import into Sketchfab.

Since UCSF-Chimera generates distinct zone/masked areas during the procedure,  we can use API scripts to hide/unhide  the areas of the cryo-EM structure directly in Sketchfab.

 Methods

Leading the way in what has been termed the “Cryo-Revolution” is the team that recently published the  near-atomic resolution of  beta-galactosidase (Subramaniam et.al. / NIH).    Thus, we thought it would meaningful to use the structure featured in the publication (EMD 2984) for the zone / masking procedure outlined below.

The 2.2 A resolution cryo-EM structure of beta-galactosidase (EMD-2984) was downloaded from EMDB website and imported into UCSF-Chimera (Figure 1).

Figure 1. EMD 2984 initial view in UCSF-Chimera

The structure includes both the cryoEM electron density map, as well as a fitted atomic model(PDB 5a1a). The model  displays as a ribbon during the initial import. The density map is a gray surface representation of the volume data. To color the individual subunits of  PDB 5a1a, we selected the “Interactive 1″ setting under the Preset menu (Presets > Interactive 1 (ribbons)) (Figure 2).

Figure 2. EMD 2984 viewed in UCSF Chimera – Assigning Colors to Subunits 

To increase the resolution of the cryo-EM structure’s surface representation, the volume viewer “step” setting was changed to 1 and the “surface level” changed to 0.03.  As shown in Figure 3, the cryo-EM structure is easily  visible using these settings and aligns  with the underlying atomic model(PDB 5a1a).

Figure 3. EMD 2984 viewed in UCSF Chimera – Increasing Resolution

The model was exported from Chimera and imported into Sketchfab, as shown in Figure 4.

Figure 4.  EMD 2984 imported into Sketchfab

 Using UCSF-Chimera Zone Feature

Though the CryoEM structure imported nicely into Sketchfab,  background particles were also present using the chosen volume viewer settings (step 1, surface level 0.03).

To examine if we could remove these background particles without  affecting the quality of the CryoEM imported into Sketchfab, we tested the  “Zone” and “Masking” feature built into UCSF-Chimera.

Step 1. The first step in this procedure is to bring up the Model Panel (Favorites > Model Panel) (Figure 5).

Figure 5. Opening the Model Panel in UCSF-Chimera

Step 2. On the Model panel, we scrolled down and open the  “Select chain(s)” feature (Favorites > Model Panel > Select chain(s))(Figure 6).

Figure 6.  Select Chain(s) Selection Tool  in UCSF-Chimera

Step 3. After clicking the Select(s) button, a pop-up window displaying  the list of PDB 5a1a chains appeared.  We checked the box next to “A” and then clicked the “Apply” button.  Once clicked, Chain A was selected on the PDB 5a1a model, as reflected by a slight greenish tint around the blue colored ribbon (Figure 7).

Figure 7. Selecting & Applying the Chain(s) 

Step 4. With the chain selected, it was now possible to generate a zone using UCSF-Chimera’s Zone Tool (Tools > Volume Data > Volume Viewer > Features > Zone) (Figure 8).

Figure 8. Bring up the Zone Tool 

 

 

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.

 Conclusions

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.

 

 

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Acknowledgments:  Mr. James Green and Mr. Corentin Metgy at Sketchfab for providing the initial API Script.

Others:

To read more about the UCSF-Chimera Zone / Masking, visit the USCF Chimera site:

Links

Citations

Publications describing the UCSF zone algorithm