A Practical Guide to Manually Fixing Protein Structures in SAMSON

For molecular modelers, working with protein structures often involves addressing various issues before diving into simulations, docking, or other workflows. Problems like missing atoms, alternate locations, or steric clashes can lead to failed simulations or inaccurate outcomes. If you prefer a fine-tuned, hands-on approach to preparing proteins, SAMSON offers powerful tools for manual fixes that ensure your structure is pristine before downstream tasks.

Why Manual Fixes Matter

While one-click preparation in SAMSON is efficient, manual adjustments provide you with complete control over the protein-cleanup process. This meticulous approach ensures that no important detail is overlooked, enabling you to handle complex structures or edge cases with precision. Whether cleaning up alternate atom locations, removing unnecessary molecules, or adding hydrogens specific to your requirements, the manual fix workflow offers a tailored solution for perfectionists.

Step-by-Step Manual Fixing

1. Remove Alternate Locations

  1. Open the Home > Validate menu and select the Alt. locations tab.
  2. Click Find alternate locations to display a list of alternate positions in your structure.
  3. Press Remove alt. locations to keep only the highest-occupancy atoms, ensuring structural clarity.

Structure validation: Alternate locations

Tip: Also check for bond lengths, non-standard residues, or steric clashes if needed. These common issues can be addressed within the Validate module for even better results.

2. Strip Ligands, Water, or Ions

  1. Navigate to Select > Biology and choose Ligands, Water, or Ions, depending on your focus.
  2. In the pop-up context toolbar, click the delete icon (erase), or use Document view > Current selection > Erase selection.

3. Add Hydrogens

  • Go to Edit > Add hydrogens to insert hydrogens automatically based on pH 7 or by residue type for standard residues. Valence rules are applied for non-standard regions.
  • If you need targeted changes, select the specific sub-structure first to limit the operation.

Note: For pH-specific protonation, consider using tools like PDBFixer (see deeper fixes). If downstream workflows require ideal hydrogen geometries, you may also need to minimize the structure.

Best Practices

  • Always validate the model after performing manual fixes to catch any missing steps.
  • For large-scale projects involving multiple proteins, consider batch preparation instead of manual fixes to save time.
  • Explore SAMSON’s extensions, like the Rotamers editor, to address steric clashes efficiently while optimizing side chains.

Take Control of Your Protein Model

Manual fixes might take a bit more time, but they provide unparalleled control over the final outcome, ensuring your input data is as reliable as possible for downstream simulations. Learn more about manual checks and fixes in SAMSON by visiting the full documentation: https://documentation.samson-connect.net/tutorials/prepare-protein/prepare-protein/.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today at https://www.samson-connect.net.

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