PySSA (Python rich client for visual protein Sequence to Structure Analysis) for Windows is a comfortable open Graphical User Interface (GUI) application combining the protein sequence to structure prediction capabilities of ColabFold with the open-source variant of the molecular structure visualization and analysis system PyMOL to make both available to the scientific end-user. PySSA enables the creation and sharing of workflow projects that comprise defined protein 3D structure predictions from their amino acid sequence, protein 3D structure alignments, as well as their visual analysis with distance diagrams or hotspot inspection. All operations can be conveniently performed by scientists without specialized computer skills or even programming knowledge on their local Windows computers, without the need for powerful GPU hardware. Thus, PySSA can help make protein structure prediction more accessible for end-users in scientific research areas like protein chemistry or molecular biology. In addition, the application is well-suited for educational purposes due to its user-friendliness and low learning curve. PySSA is openly available on GitHub, alongside a convenient installer executable for the Windows operating system: https://urban233.github.io/PySSA/install.html. To demonstrate its capabilities, the usage of PySSA in a protein mutation study on the protein drug Bone Morphogenetic Protein 2 (BMP2) is described: the structure prediction results indicate that the previously reported BMP2-2Hep-7M mutant, which is intended to be less prone to aggregation, does not exhibit significant spatial rearrangements of amino acid residues interacting with the receptor.