Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 14646123

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments.

Yurii Gaponov·Noriyuki Igarashi·Masahiko Hiraki·Kumiko Sasajima·Naohiro Matsugaki·Mamoru Suzuki·Takashi Kosuge·Soichi Wakatsuki
View original source ↗Export metadata ↓

Abstract

A control system for high-throughput protein crystallography experiments has been developed based on a multilevel secure (SSL v2/v3) UNIX socket under the Linux operating system. Main features of protein crystallography experiments (purification, crystallization, loop preparation, data collecting, data processing) are dealt with by the software. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data, that are stored in Network File Server) in a relational database (MySQL). The system consists of several servers and clients. TCP/IP secure UNIX sockets with four predefined behaviors [(a) listening to a request followed by a reply, (b) sending a request and waiting for a reply, (c) listening to a broadcast message, and (d) sending a broadcast message] support communications between all servers and clients allowing one to control experiments, view data, edit experimental conditions and perform data processing remotely. The usage of the interface software is well suited for developing well organized control software with a hierarchical structure of different software units (Gaponov et al., 1998), which will pass and receive different types of information. All communication is divided into two parts: low and top levels. Large and complicated control tasks are split into several smaller ones, which can be processed by control clients independently. For communicating with experimental equipment (beamline optical elements, robots, and specialized experimental equipment etc.), the STARS server, developed at the Photon Factory, is used (Kosuge et al., 2002). The STARS server allows any application with an open socket to be connected with any other clients that control experimental equipment. Majority of the source code is written in C/C++. GUI modules of the system were built mainly using Glade user interface builder for GTK+ and Gnome under Red Hat Linux 7.1 operating system.

Explore related subjects

CrystallographyDatabase Management SystemsDatabases, ProteinFeedbackInformation Storage and RetrievalInternetProgramming LanguagesProteinsRoboticsSoftwareSoftware DesignUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Yurii Gaponov, Noriyuki Igarashi, Masahiko Hiraki, Kumiko Sasajima, Naohiro Matsugaki, Mamoru Suzuki, Takashi Kosuge, Soichi Wakatsuki. 2003-11-28. Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments.. https://doi.org/10.1107/s0909049503023458

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

The same but different: isomorphous methods for phasing and high-throughput ligand screening.

Isomorphous difference methods allow rapid and detailed visualization of localized changes in macromolecular structures, whether as a result of mutation or the binding of ligands. Practical aspects of isomorphous methods and differential crystallography are presented, particularly in their application to the phasing of new structures by multiple isomorphous replacement and the detection and characterization of ligand binding. Techniques for maintaining isomorphism between crystals to maximize the differential signal are covered, as are the computational steps involved in generating difference electron density maps. Frontier applications such as determining single-site ligand-binding affinities crystallographically, high-throughput screening of combinatorial compound libraries, in crystallo competition assays, and inferring protein function via exogenous ligand-binding screens are discussed.

Crystallography↗
PubMed2007

Crystallographic software: a sustainable resource for the community.

Virtually all software is constantly changing and evolving (and crystallographic software is no exception), which makes it nearly impossible to write a chapter that will remain current. In this chapter, we introduce CRYSTAL, a website (http://crystal.uvm.edu) where a comprehensive list of available crystallographic packages for each step of macromolecular structure determination will be maintained. Additionally, we provide links to books, journals, and a number of educational sites on crystallography. For each program/site included at CRYSTAL, a detailed description will include: the most current version, the authors, and appropriate operating systems to host the program. Links to download the programs, available tutorials, and references to cite when using the program/site are also provided.

Crystallography↗
PubMed2006

Architecture of fiber network: from understanding to engineering of molecular gels.

A new approach of engineering of molecular gels was established on the basis of a nucleation-initiated network formation mechanism. A variety of gel network structures can be obtained by regulating the starting temperature of the sol-gel transition. This enables us to tune the network from the spherulitic domains pattern to the extensively interconnected fibrillar network. As the consequence of fibrous network structure turning, desirable rheological and other in-use properties of the materials can be obtained accordingly. This approach of micro-/nanostructural fabrication may open up a new route for micro-/nanofunctional materials engineering in general.

Crystallography↗