EPR Toolbox
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PDB Splitter

Feature implemented in EPRtoolbox or download now PDBs are great, however from time to time you only actually want one protein chain to analyse at a time. What you need to do then is split the PDB of many chains into separate PDB files.

This MATLAB script does exactly that. Using local .pdb files (selectable via an open window) or files directly from rcsb.org (using PDB identifier code) up to 4 chains (in this current version) are exported to the current work folder. Important note: This script does use pdbread and pdbwrite from the Mathworks Bioinformatics Toolbox. This is not the ideal open source script I wish it could be, but this is largely due to the widely varying PDB format. I intend to look over how Jescke and Polyhach solve this problem in MMM and perhaps update this script at a later date.

This page previously appeared on morganbye.net[^1][^2][^3]

[^1:] http://morganbye.net/pdb-splitter [^2:] http://morganbye.net/eprtoolbox/pdb-splitter) [^3:] http://morganbye.net/uncategorized/2012/01/pdb-splitter

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Power Saturation Curves

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EPR Toolbox
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EasyRefiner

Faced with fitting well over 30 experiments at room and low temperature at multiple frequencies, as all of my experiments are spin-labelled mutants of the same protein then surely their EPR properties would be similar. I decided that there must be a …

EPR Toolbox
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e2af

E2AF or “EPR 2 ASCII folder” is a folder version of E2A, whereby a folder of Bruker EPR files are converted to ASCII data files (readable by any operating system), by default the conversion is to *.csv files (comma separated values). …

EPR Toolbox
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Savitzky-Golay - sgol

The Savitzky-Golay smoothing function essentially applies a local polynominal fitting routine to a series of data points to then find the smoothed data points. This has the benefit that for sharp intense peaks (common to EPR) that the line broadening …

LEADERSHIP, SCALE, AND THE HUMAN ELEMENT

Principles & Perspectives

How do you define successful engineering leadership?

The Philosophy

Many view technical leadership as being the “smartest architect in the room.” I see it as the opposite. My job is to build a room where I don’t have to be the smartest person because the systems, culture, and communication are so robust that the team can out-innovate me.

The Strategy

  • Alignment: Does every engineer understand how their sprint task impacts the company’s bottom line?
  • Velocity vs. Stability: We aren’t just “shipping fast”; we are building a predictable, repeatable engine that doesn’t collapse under its own weight at the next order of magnitude.
  • The Human Growth Curve: Success is when the engineering team’s capability evolves faster than the product’s complexity. If the team feels stagnant, the tech stack will soon follow.

What is your approach to scaling technical organizations?

The Philosophy

Scaling isn’t just “hiring more people” - that’s often how you slow down. Scaling is about moving from Individual Heroics to Organizational Systems.

The Strategy

  • The 3-Continent Perspective: Having managed global teams, I focus on “High-Signal Communication.” As you grow, the cost of a meeting triples. I implement “Asynchronous-First” cultures that protect deep-work time while ensuring no one is blocked by a timezone.

  • Modular Autonomy: I advocate for breaking down monolithic teams into autonomous units with clear ownership. This reduces the “communication tax” and allows us to scale the headcount without scaling the bureaucracy.

  • Automation as Infrastructure: At petabyte scale, manual intervention is a failure. I treat the developer experience (CI/CD, observability, self-service infra) as a first-class product to keep the “path to production” frictionless.

How do you balance high-growth velocity with technical stability?

The Philosophy

Technical debt isn’t a “bad thing” to be avoided; it’s a set of historical decisions that no longer serve you. Like any loan, leverage can accelerate growth when investments payoff. But if velocity and returns are slowing you need a payment plan before the interest kills you.

The Strategy

  • The ROI Filter: I don’t refactor for the sake of “clean code.” I don’t refactor a micro-service with no users. I refactor when the pain on that debt - measured in bugs, downtime, or developer frustration - starts to exceed the cost of the fix.

  • Zero-Downtime Culture: Especially at scale, stability is a feature. I implement “Guardrail Engineering” where the system is designed to fail gracefully, ensuring that a Series B growth spike becomes a success story rather than a post-mortem.

  • The 70/20/10 Rule: I typically aim to dedicate 70% of resources to new features, 20% to infrastructure/debt, and 10% to R&D. This ensures we never stop innovating, but we never stop fortifying either.