Design Demo Fails After MCP Registration and Python Script Execution Also Errors

[wanghan0501]

Problem Description:

I encountered two issues while using the BindCraft MCP server:

1. MCP Registration Issue:​ After following the Docker quick start guide in the README and successfully registering the MCP server with Claude Code, attempting to run the design demo fails to work correctly.
2. Python Script Execution Issue:​ Directly running the local Python script also results in an error with the following command:
   python clean_scripts/use_case_1_quick_design.py --input examples/data/PDL1.pdb --output results/quick_design

Expected Behavior:

1. After successful MCP server registration, all 5 BindCraft tools should be usable normally within Claude Code.
2. Direct execution of the Python script should successfully run the protein binder design pipeline.

Actual Behavior:

1. MCP tools fail to work after registration.
2. Direct execution of the Python script also throws an error.