Feature request: Update Chimera and PyMol Functions to Show ClinVar Variants as Spheres

[berntpopp]

Description

The current Chimera script generated by the pipeline visualizes pathogenicity using color coding based on predictions. However, it does not visually differentiate ClinVar variants. This issue proposes an enhancement to the Chimera script to display ClinVar variants as spheres, allowing users to easily distinguish these important variants on the structure.

Proposed Solution

• Modify the generate_chimera_session function to include logic for identifying ClinVar variants.
• Use Chimera's represent sphere command to render ClinVar variant residues as spheres.
• Ensure the script handles multiple ClinVar variants, properly visualizing each one as a sphere.
• Make the representation color-configurable via config.json to allow users to choose the color of the spheres.

Acceptance Criteria

• ClinVar variants are visually distinguished as spheres in the Chimera script.
• The feature works seamlessly alongside existing pathogenicity color coding.
• The sphere representation color is configurable via config.json.
• The Chimera session correctly loads and displays the spheres without errors.

Additional Notes

• Consider adding a legend or annotations in the Chimera session to clarify the meaning of the spheres.
• Update relevant documentation to reflect the changes in Chimera script generation.