PyBmw v1.2 — SAVES Integration, Better Rotamer Workflow, and Smarter Batch Mutations

🚀 PyBmw v1.2 is now officially live!

This update focuses on making mutation workflows smoother, clearer, and easier to share or validate.
If you’ve been using PyBmw for course work, structural analysis, or protein design pipelines, this version should feel more stable and natural to work with.

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🆕 What's New in v1.2

SAVES v6.0 Upload (Built-In)

You can now directly upload your mutated structure to the UCLA SAVES validation server from inside the plugin.
No browser copy-paste, no exporting required.

The plugin will also auto-install its web dependencies (requests + beautifulsoup4) the first time it's run — so researchers don’t need to handle Python setup manually.

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Improved Step-by-Step Rotamer Workflow

The step-wise mutation interface feels more fluid now:

• Clear current_rotamer / total_rotamers indicator
• Next / Previous rotamer navigation is smoother
• Optional sculpt refinement cycles are cleaner to configure

Useful if you prefer to visually inspect every mutation.

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Better Coloring, Highlighting & Labels

When selecting multiple chains or large sets of residues:

• Each chain is now highlighted in a different color
• Staged mutations are easier to distinguish
• Final mutated residues remain cyan and neatly labeled, e.g.:

HIS58 → ALA

Everything is readable without overcrowding the structure.

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More Forgiving CSV Import

The CSV parser now handles:

• lowercase amino acid codes
• inconsistent spacing
• extra commas
• chain+residue formats like A123 or A 123

Basically, if your CSV looks human, PyBmw will interpret it correctly.

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Exporting Made Clearer

Choose what you want to save:

• PDB only
• PyMOL session only
• or both in your selected folder

If steric clashes are detected, the plugin will politely warn you instead of silently exporting messy results.

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💡 Why This Update Matters

This release is about reducing friction during structural modeling work.
The plugin now plays nicer in teaching labs, shared workstations, and environments where users can’t install Python packages.

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📦 Get the Plugin

Everything you need (including install instructions and screenshots) is available in the main repo:

https://github.com/protmind/Python-Batch-Mutation-Wizard-PyBmw-

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If you run into anything weird, have a feature idea, or want to collaborate — just open an issue or reach out.
This tool grows through actual use and actual feedback.

Full Changelog: v1.0...v1.2

PyBmw v1.0 - Initial Public Release

🚀 We are thrilled to announce the first official public release of the Python Batch Mutation Wizard (PyBmw) v1.0!

This initial version provides a robust and user-friendly GUI to significantly accelerate in-silico mutagenesis workflows directly within PyMOL. PyBmw is designed for both single-site precision and high-throughput batch processing.

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✨ Key Features in this Release

• Multiple Mutation Modes:

  • Batch Mode: Apply a single mutation to all selected residues at once.
  • Individual Mode: Assign a unique mutation to each selected residue in a clean table.
  • Step-by-Step Mode: Sequentially apply mutations, with interactive controls to preview and cycle through rotamers.

• High-Throughput CSV Import:

  • Load and stage hundreds of mutations directly from a simple, two-column CSV file (Chain ResidueID,TargetAA).

• Advanced Refinement:

  • Engage PyMOL's sculpting algorithm to refine sidechain conformations and find better fits.

• Clear Visual Feedback:

  • Highlighting: Staged residues are highlighted for clear identification.
  • Coloring & Labeling: Mutated residues are automatically colored cyan and labeled (e.g., "ALA123 -> TRP").

• Flexible Exporting:

  • Save your results as a clean PDB file, a full PyMOL Session (.pse), or both.

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🔧 Getting Started

To install and use the plugin, please refer to the detailed instructions in our main README.md file.

A huge thank you to everyone involved in the development and testing of this initial version!