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<!DOCTYPE html>
<html lang="en">
<head>
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<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Software — Thomas C. Terwilliger</title>
<meta name="description" content="Software developed by Thomas C. Terwilliger: Phenix, SOLVE, RESOLVE, and related tools for macromolecular structure determination.">
<link rel="canonical" href="https://www.thomasterwilliger.org/software.html">
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</head>
<body>
<div class="page-wrapper">
<!-- ===== HEADER ===== -->
<header class="site-header">
<div class="container">
<div class="header-content">
<img src="images/Terwilliger_Thomas_Portrait.jpg" alt="Thomas C. Terwilliger" class="photo">
<div class="header-text">
<h1>Thomas C. Terwilliger</h1>
<p class="tagline">Structural Biology · Crystallography · Cryo-EM · Computational Methods</p>
<p class="affiliation">
<a href="https://www.phenix-online.org/">Phenix</a> Software Team · <a href="https://newmexicoconsortium.org/">New Mexico Consortium</a><br>
Los Alamos National Laboratory Fellow (Retired)
</p>
</div>
</div>
</div>
<nav class="site-nav">
<div class="container">
<a href="index.html">Home</a>
<a href="publications.html">Publications</a>
<a href="software.html" class="active">Software</a>
<a href="bio.html">Biography</a>
<a href="group.html">Group</a>
<a href="news.html">News</a>
<a href="presentations.html">Presentations</a>
<a href="links.html">Links</a>
</div>
</nav>
</header>
<!-- ===== MAIN ===== -->
<main>
<div class="content-section">
<div class="container">
<h2 class="page-title">Software</h2>
<div class="software-card">
<h2>Phenix</h2>
<p>
Phenix (Python-based Hierarchical ENvironment for Integrated Xtallography)
is a comprehensive system for macromolecular structure determination
using X-ray crystallography, cryo-electron microscopy, and neutron diffraction.
Phenix includes automated tools for experimental phasing, molecular replacement,
model building, refinement, validation, and ligand fitting.
</p>
<p>
Recent Phenix developments include integration of AlphaFold predictions
into experimental structure determination, density modification of cryo-EM maps,
automated model building from cryo-EM maps, and map improvement tools.
</p>
<a href="https://www.phenix-online.org/" class="sw-link">Visit phenix-online.org</a>
</div>
<div class="software-card">
<h2 id="solve-resolve">SOLVE & RESOLVE</h2>
<p>
SOLVE and RESOLVE were developed by Tom Terwilliger at Los Alamos
National Laboratory beginning in the mid-1990s. Together they formed
a complete pipeline for macromolecular crystal structure determination
— from experimental phasing through density modification and automated
model building.
</p>
<p>
<b>SOLVE</b> was the first fully automated software for macromolecular
structure analysis using experimental phasing. It introduced probabilistic
approaches to heavy-atom parameter estimation, correlated phasing of
multiple isomorphous replacement and anomalous diffraction datasets, and
automated decision-making in structure solution. SOLVE supported MAD,
SAD, MIR, and SIR methods, making experimental phasing accessible to
non-specialist users.
</p>
<p>
<b>RESOLVE</b> was the first likelihood-based system for
density modification and one of the early automated model building
tools. It introduced maximum-likelihood density modification, automated
model building by template matching and iterative fragment extension,
and prime-and-switch phasing to reduce model bias. RESOLVE could
automatically build and refine protein models starting from experimental
electron density maps.
</p>
<p>
The methods in SOLVE and RESOLVE have been incorporated into
the <a href="https://www.phenix-online.org/">Phenix</a> software suite,
where they continue to be developed and extended. The Phenix AutoSol
wizard is essentially the next generation of the SOLVE and RESOLVE
algorithms for automated experimental phasing, density modification,
and model building. SOLVE and RESOLVE can still be run as standalone
programs for users who prefer the original interfaces.
</p>
<a href="images/solve_documentation.pdf" class="sw-link">SOLVE/RESOLVE Archival Documentation (PDF)</a>
</div>
</div>
</div>
</main>
<!-- ===== FOOTER ===== -->
<footer class="site-footer">
<div class="container">
Contact: <a href="mailto:tterwilliger@newmexicoconsortium.org">tterwilliger@newmexicoconsortium.org</a><br>
This site preserves scientific materials originally hosted at solve.lanl.gov.<br>
Last updated 2026
</div>
</footer>
</div>
</body>
</html>