A real user wants to evaluate an X-ray crystal structure using MolProbity. Navigate to the 'Evaluate X-ray' page. What are the primary methods for inputting a PDB file? After inputting, what are the key steps or options presented to the user before the analysis begins? List at least three distinct input methods and three key pre-analysis options/steps.
Navigate to 'molprobity.biochem.duke.edu'. Click on the 'Evaluate X-ray' link (ID 21). Identify and list the different methods provided for inputting a PDB file. Identify and list at least three key options or steps presented to the user *before* the structure analysis process begins (e.g., related to adding hydrogens, specifying resolution, or chain selection).
The agent successfully navigates to the 'Evaluate X-ray' page. The agent identifies at least three PDB input methods, such as 'Upload from local disk', 'Retrieve from PDB by ID', and 'Paste PDB text'. The agent identifies at least three pre-analysis options or steps, such as 'Add hydrogens', 'Specify resolution', 'Remove unwanted chains', or 'Specify chain(s) to analyze'.