ARP/wARP and molecular replacement: the next generation

Automatic iterative model (re‐)building, as implemented in ARP/wARP and its new control system flex‐wARP, is particularly well suited to follow structure solution by molecular replacement. More than 100 molecular‐replacement solutions automatically solved by the BALBES software were submitted to thr...

Full description

Saved in:
Bibliographic Details
Published in:Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2008-01, Vol.64 (1), p.49-60
Main Authors: Cohen, Serge X., Ben Jelloul, Marouane, Long, Fei, Vagin, Alexei, Knipscheer, Puck, Lebbink, Joyce, Sixma, Titia K., Lamzin, Victor S., Murshudov, Garib N., Perrakis, Anastassis
Format: Article
Language:English
Subjects:
Algorithms
ATOMS
Biochemistry, Molecular Biology
Computer Science
Computer Vision and Pattern Recognition
CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY
Crystallography, X-Ray
Databases, Protein
DENSITY
ELECTRON DENSITY
ELECTRONS
EVOLUTION
FOCUSING
Life Sciences
Machine Learning
MATHEMATICAL SOLUTIONS
model building
Models, Molecular
molecular replacement
Proteins - chemistry
refinement
Research Papers
Software
SOLUTIONS
Statistics
Structural Biology
Ubiquitin-Conjugating Enzymes - chemistry
Citations: Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Automatic iterative model (re‐)building, as implemented in ARP/wARP and its new control system flex‐wARP, is particularly well suited to follow structure solution by molecular replacement. More than 100 molecular‐replacement solutions automatically solved by the BALBES software were submitted to three standard protocols in flex‐wARP and the results were compared with final models from the PDB. Standard metrics were gathered in a systematic way and enabled the drawing of statistical conclusions on the advantages of each protocol. Based on this analysis, an empirical estimator was proposed that predicts how good the final model produced by flex‐wARP is likely to be based on the experimental data and the quality of the molecular‐replacement solution. To introduce the differences between the three flex‐wARP protocols (keeping the complete search model, converting it to atomic coordinates but ignoring atom identities or using the electron‐density map calculated from the molecular‐replacement solution), two examples are also discussed in detail, focusing on the evolution of the models during iterative rebuilding. This highlights the diversity of paths that the flex‐wARP control system can employ to reach a nearly complete and accurate model while actually starting from the same initial information.
ISSN:1399-0047
0907-4449
2059-7983
1399-0047
2059-7983
DOI:10.1107/S0907444907047580