J. Appl. Cryst.の発刊に際して

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Iterative model-building, structure refinement, and density modification with the PHENIX AutoBuild Wizard Thomas C. Terwilliger a* , Ralf W. Grosse-Kunstleve b , Pavel V. Afonine b , Nigel W. Moriarty b , Peter Zwart b , Li-Wei Hung a , Randy J. Read c , Paul D. Adams b* a b Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720, USA. c Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK. * Email: terwill@lanl.gov or PDAdams@lbl.gov Running title: The PHENIX AutoBuild Wizard Abstract The PHENIX AutoBuild Wizard is a highly automated tool for iterative model- building, structure refinement and density modification using RESOLVE or TEXTAL model- building, RESOLVE statistical density modification, and phenix.refine structure refinement. Recent advances in the AutoBuild Wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model completion algorithms, and automated solvent molecule picking. Model completion algorithms in the AutoBuild Wizard include loop-building, crossovers between chains in different models of a structure, and side-chain optimization. The AutoBuild Wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 A to 3.2 A, resulting in a mean R-factor of 0.24 and a mean free R factor of 0.29. The R-factor of the final model is dependent on the quality of the starting electron density, and relatively independent of resolution. Keywords: Model building; model completion; macromolecular models; Protein Data Bank; structure refinement; PHENIX Introduction Iterative model-building and refinement is a powerful approach to obtaining a complete and accurate macromolecular model. The approach consists of cycles of building an atomic model based on an electron density map for a macromolecular structure, refining the structure, using the refined structure as a basis for improving the map, and building a new model. This type of approach has been carried out in a semi-automated fashion for many years, with manual model-building iterating with automated refinement (Jensen, 1997). More recently, with the development first of ARP/wARP (Perrakis et al., 1999), and later other procedures including RESOLVE iterative model-building and refinement (Terwilliger,

Iterative model-building, structure refinement, and density modification with the PHENIX AutoBuild Wizard

The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.

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DIALS: implementation and evaluation of a new integration package

Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors

CrystFEL is a suite of programs for processing data from `serial crystallography' experiments, which are usually performed using X-ray free-electron lasers (FELs) but also increasingly with other X-ray sources. The CrystFEL software suite has been under development since 2009, just before the first hard FEL experiments were performed, and has been significantly updated and improved since then. This article describes the most important improvements which have been made to CrystFEL since the first release version. These changes include the addition of new programs to the suite, the ability to resolve `indexing ambiguities' and several ways to improve the quality of the integrated data by more accurately modelling the underlying diffraction physics.

/pdf/recent-developments-in-crystfel-27lt55p1oc.pdf

Recent developments in CrystFEL.

https://journals.iucr.org/m/issues/2014/04/00/it5001/it5001.pdf

Room-temperature macromolecular serial crystallography using synchrotron radiation.

In this work, we propose a framework called Auto-Assembly for automated robotic assembly from design files and demonstrate a practical implementation on modular parts joined by fastening using a robotic cell consisting of two robots. We show the flexibility of the approach by testing it on different input designs. Auto-Assembly consists of several parts: design analysis, assembly sequence generation, bill-of-process (BOP) generation, conversion of the BOP to control code, path planning, simulation, and execution of the control code to assemble parts in the physical environment.

Fedor Chervinskii

Papers

Recent developments in CrystFEL.

Room-temperature macromolecular serial crystallography using synchrotron radiation.

Auto-Assembly: a framework for automated robotic assembly directly from CAD