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introduction

Open Access

Model building, refinement and validation

Roberto A. Steiner,  Bernhard Rupp, 
  • Pages: 325-327
  • First Published: 05 April 2012

research papers

Open Access

Completion of autobuilt protein models using a database of protein fragments

Kevin Cowtan, 
  • Pages: 328-335
  • First Published: 05 April 2012
Open Access

Practical structure solution with ARCIMBOLDO

Dayté Rodríguez,  Massimo Sammito,  Kathrin Meindl,  Iñaki M. de Ilarduya,  Marianus Potratz,  George M. Sheldrick,  Isabel Usón, 
  • Pages: 336-343
  • First Published: 05 April 2012
Open Access

Conventions and workflows for using Situs

Willy Wriggers, 
  • Pages: 344-351
  • First Published: 05 April 2012
Open Access

Towards automated crystallographic structure refinement with phenix.refine

Pavel V. Afonine,  Ralf W. Grosse-Kunstleve,  Nathaniel Echols,  Jeffrey J. Headd,  Nigel W. Moriarty,  Marat Mustyakimov,  Thomas C. Terwilliger,  Alexandre Urzhumtsev,  Peter H. Zwart,  Paul D. Adams, 
  • Pages: 352-367
  • First Published: 05 April 2012
Open Access

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

Oliver S. Smart,  Thomas O. Womack,  Claus Flensburg,  Peter Keller,  Włodek Paciorek,  Andrew Sharff,  Clemens Vonrhein,  Gérard Bricogne, 
  • Pages: 368-380
  • First Published: 05 April 2012
Open Access

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Jeffrey J. Headd,  Nathaniel Echols,  Pavel V. Afonine,  Ralf W. Grosse-Kunstleve,  Vincent B. Chen,  Nigel W. Moriarty,  David C. Richardson,  Jane S. Richardson,  Paul D. Adams, 
  • Pages: 381-390
  • First Published: 05 April 2012
Open Access

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

Axel T. Brunger,  Debanu Das,  Ashley M. Deacon,  Joanna Grant,  Thomas C. Terwilliger,  Randy J. Read,  Paul D. Adams,  Michael Levitt,  Gunnar F. Schröder, 
  • Pages: 391-403
  • First Published: 05 April 2012
Open Access

Low-resolution refinement tools in REFMAC5

Robert A. Nicholls,  Fei Long,  Garib N. Murshudov, 
  • Pages: 404-417
  • First Published: 05 April 2012
Open Access

Tetartohedral twinning could happen to you too

Pietro Roversi,  Eric Blanc,  Steven Johnson,  Susan Mary Lea, 
  • Pages: 418-424
  • First Published: 05 April 2012
Open Access

Handling ligands with Coot

Judit É. Debreczeni,  Paul Emsley, 
  • Pages: 425-430
  • First Published: 05 April 2012
Open Access

JLigand: a graphical tool for the CCP4 template-restraint library

Andrey A. Lebedev,  Paul Young,  Michail N. Isupov,  Olga V. Moroz,  Alexey A. Vagin,  Garib N. Murshudov, 
  • Pages: 431-440
  • First Published: 05 April 2012
Open Access

Challenges and surprises that arise with nucleic acids during model building and refinement

William G. Scott, 
  • Pages: 441-445
  • First Published: 05 April 2012
Open Access

Use of noncrystallographic symmetry for automated model building at medium to low resolution

Tim Wiegels,  Victor S. Lamzin, 
  • Pages: 446-453
  • First Published: 05 April 2012
Open Access

Statistical quality indicators for electron-density maps

Ian J. Tickle, 
  • Pages: 454-467
  • First Published: 05 April 2012
Open Access

To B or not to B: a question of resolution?

Ethan A. Merritt, 
  • Pages: 468-477
  • First Published: 05 April 2012
Open Access

Implementing an X-ray validation pipeline for the Protein Data Bank

Swanand Gore,  Sameer Velankar,  Gerard J. Kleywegt, 
  • Pages: 478-483
  • First Published: 05 April 2012
Open Access

PDB_REDO: constructive validation, more than just looking for errors

Robbie P. Joosten,  Krista Joosten,  Garib N. Murshudov,  Anastassis Perrakis, 
  • Pages: 484-496
  • First Published: 05 April 2012