ResLog Analysis, Generate Mask and Align 3D Maps explained
Several new tools in cryoSPARC make for an easier experiment workflow.
This feature generates plots that show how the resolution of a given structure increases as more particles are added to the reconstruction. This insight may be useful in determining whether a higher-resolution result is possible with more particles, or if fewer particles are needed to achieve the same resolution.
From the Experiments page, select the Particles associated with the result of a previous refinement experiment.
Choose New Experiment > ResLog Analysis. Click Launch and Enqueue to commence the analysis. Once complete, the plots will appear directly on the Launch page.
Use this tool to select a region you wish to focus on in Refinement, while setting aside portions of the 3D density map that are unstructured or irrelevant for your experiment, e.g., a micelle or nanodisc.
To use the Generate Mask feature, select one structure from the result of a previous Refinement experiment.
Choose New Experiment > Generate Mask. Click on the Setup button on the left-hand sidebar to adjust parameters.
By default, the Threshold Value parameter (
genmask_thresh) is set to "null", and it must be changed.
The Threshold Value can either be an absolute or relative input. If Threshold value is fraction of max? (
genmask_thresh_relative) is set to "false", then Threshold Value must be the absolute density value at which the previously refined input structure is thresholded for application of the mask. Subject to mask dilation, discussed below, any region with a density greater than the inputted Threshold Value will then be included in the mask, and any region with a density below the Threshold Value will be excluded from the mask. You can determine an appropriate Threshold Value by examining the density profile of the previously refined structure in a tool such as USCF Chimera.
If Threshold value is fraction of max? (
genmask_thresh_relative) is set to "true", then Threshold Value must be a value between 0 and 1, reflecting a fraction of the maximum density of the input structure. In this case, you will likely need to estimate the Threshold Value.
Adjust the Mask dilation far (A) (
genmask_dist_far_ang) and Mask dilation near (A) (
genmask_dist_near_ang) parameters if desired. Mask dilation near means that the mask created by setting the Threshold Value will be expanded by that number of angstroms. Between the value for Mask dilation near and Mask dilation far, the mask has a soft fall off.
Click Launch and Enqueue to generate the mask. Once complete, you can download the masked result directly from the Launch page in order to view it.
You may then proceed to select the generated Mask from the Experiments page, along with one or more Structures and Particle sets to perform a further Refinement experiment.
Align 3D Maps
Use this tool to align 3D maps to a common reference in order to better analyze maps obtained from different experiments. Select two or more structures from the result of a previous experiment, then choose New Experiment > Align 3D Maps.
The maps need not come from the same type of experiment - in this example, we wanted to align the coarse-resolution map obtained from an Ab-initio Reconstruction with the higher-resolution map obtained from a Refinement experiment.
Once complete, download the aligned maps directly from the Launch page.
New to cryoSPARC? Check out our Workflow Series posts here:
- 2D Classification
- Ab-Initio Reconstruction
- Homogeneous Refinement
- Heterogeneous Refinement