Cryo-EM Structures into Sketchfab – Manual Noise Reduction Using 3DS Max

Method of reducing noise and importing Cryo-EM data into Sketchfab using 3DS Max

by Sketchfab For Science

Summary:

Molecular viewers and analysis software such as UCSF Chimera and EMD Astex are used throughout the scientific community to interactively study structures being discovered by Cryo-EM (ref 1) .

Most of these viewers have built-in tools to help generate the best signal-to-noise ratio (ref 2).  In many cases, however, higher resolution settings  leads to an increase in background noise (ref 3).

For importing into Sketchfab, we have explored if it was possible to remove background particle noise from cryo-em structures directly in 3DS Max . Overall, we find that if the input cryo-em strucure has a solid mesh, the background particles can be selected and removed using the polygon selection tools found in most professional 3D animation software packages.

 

Methods

EMD-3109 was viewed in the Open Astex Viewer directly on the Visualization link of the EMDataBank website.  A screen capture of the latter is shown in Figure 1. The author(s) recommended contour level for this map is 0.120.

 

Figure 1. EMD 3109 as viewed in Open Astex Viewer

 As one increases the resolution, incredible structure is revealed on the virus.  However, background noise also increases.   Similar results were obtained by importing EMD 3109 directly into USCF Chimera (see Figure 2).

Figure 2. EMD 3109 viewed in UCSF Chimera

To test if we could separate background noise from the actual structure being studied, we exported models from Chimera using a series of signal -to-noise settings.  Next, we imported these files into various 3D animation packages to see if we could detach the solid mesh objects from background particles.

Results

EMD 3109 was exported from Chimera in various formats (.dae, .obj, .stl) and  imported into 3DS Max. Using the mesh editing tools, we found we could select and detach the viral structure (solid mesh object) from the background particle meshes.   Once detached, the solid model could be separated from the background particles.  An interactive animation of the process is seen in Figure 3.

Figure 3.  Detaching Solid Mesh Objects from Particles.

After hiding or deleting the background meshes, the individual viral structure was exported as an .obj file and uploaded to Sketchfab (shown  in  Fig. 4)

Figure 4.  EMD 3109 (minus background particles) imported into Sketchfab.

Modifying EMD files for any reason should be treated with care, as these outputs represent a process of discovery, not just an end-point. As seen in Figure 3,  it is possible to upload the  background mesh and structure into SF directly from 3DS Max (even with added  polygon count).  Thus, we explored ways to simply hide the background mesh directly in the SF application.

Using a API provide by Mr. James Green and Mr. Corentin Metgy at Sketchfab, one can now hide the background from the primary EMD structure directly in the SF application (Fig. 5).   This was accomplished by naming the structure and background objects in 3DS Max and adjusting the API script accordingly.

Figure. 5  Hiding EMD 3019 Background Mesh

 Conclusions

While many viewers are available, it is sometimes difficult to see Cryo-EM structures at the author recommend viewing level without the background noise obscuring the structure.  The method described here helps to solve this problem via 1) exporting from UCSF-Chimera 2)  detaching the background mesh in 3D animation software and 3) uploading the detached model(s) to Sketchfab.

This method can also be used with surface-colored structures (data not shown).  In this case, you simply need to adjust the volume settings to take into account the added background mesh volume.

Working with near-atomic resolution structures, we find the above method does not work at extremely high resolution settings.  It was not possible to separate the background particles from the structure using the polygon select tools in 3DS Max.

However,  researchers in the field have found a way to reduce background noise of their near-atomic resolution structures directly in UCSF-Chimera using the zone / masking tool.   This method will be discussed in the near future.