Repair and validate a structure
Follow one structure from input through two analyses to a shared result.
This tutorial connects two analyses: repair a structure with PDBFixer, then inspect the repaired structure with MolProbity. Along the way, you will save an output, reuse it as an input, and share the final result.
You need an account with permission to submit jobs and enough workspace credits for both runs. Each submission shows its own cost. The example teaches the product flow; the settings are not a universal preparation protocol for your research structures.
Choose the workspace and structure
Check the active workspace in the account menu. Both runs should belong to the workspace where you intend to keep and share the work.
Use the public 1HSG structure record for this exercise. It contains a protease complex with a bound ligand. Keep the identifier with your notes so the starting structure remains identifiable.
Submit the repair
Open PDBFixer and load 1HSG through its RCSB PDB input method. Alternatively, download the PDB file from the source record and upload it under PDB. Wait for the input to load before submitting.
Set Job name to 1HSG repair tutorial. Check these settings:
- Heterogens: Keep all (ligands, ions, water).
- Add missing heavy atoms: On.
- Add missing hydrogens: On, with pH value set to
7. - Add missing residues: Off.
- Prepare for molecular dynamics: Off.
- Replace nonstandard residues: Off.
Under Advanced settings, keep Output format set to PDB, leave Remove chains and Apply mutations empty, and leave Add solvent box and Add lipid membrane off.
Review the displayed cost and select Submit job. Keep the job URL. You can leave the page while it runs and return through Results.
Inspect and save the repaired structure
When the job finishes, inspect Viewer and Data. Check that the output is associated with the input you submitted and review Processing applied. A successful repair does not mean every geometric problem has been corrected.
Open the result's Files view:
- Choose Select files.
- Select the repaired
.pdbfile. Do not select the summary CSV or settings JSON as the next tool's structure input. - Choose Save to Files.
Open the Files library and confirm that the saved structure appears. Download the repaired structure and the job's summary and settings files if you want an independent local record. A saved library entry still depends on its source job, so deleting that job also removes the saved output.
Validate the saved output
In the library, open the repaired file's actions menu and choose Send to tool:
- Choose MolProbity from the compatible destinations.
- Review the assignment to Protein Structure.
- Select Send to MolProbity to open the tool page.
- Check that the input is the repaired file, then set Job name to
1HSG repaired structure validation. - Review the new credit cost and select Submit job.
Sending the file opens the form; it does not submit the analysis automatically. If the expected destination is absent, check that you selected the repaired coordinate file rather than a report or archive.
Read the validation result
When MolProbity completes, open Validation metrics. Read each measurement with its unit, status, and description. Open Outliers for the reported locations and details.
Keep the repair job and validation job together in your research record. The validation describes the repaired structure used as input; it is not a before-and-after comparison with the original structure. Such a comparison requires a separate validation of the original under comparable conditions.
Completion confirms that the software ran. Use the reported measurements and the tool's documentation to assess the structure, rather than treating the completed status as a scientific approval.
Share the validation result
As the submitter, open Share in the validation job's output panel. For a specific external reader, select Invited only, enter their email, and select Add. Adding the invitation applies that visibility and sends the invitation; check the recipient list before copying the result link.
For colleagues already in the workspace, Private visibility already permits workspace access. The sharing and permissions guide explains other audiences and restricted files.
Send both job links when a reader needs the repair history as well as the validation. Sharing the validation job alone does not grant access to a separate private repair job. Download the reports and structures you need to retain before deleting either job.