Topic
Software
About: Software is a research topic. Over the lifetime, 130577 publications have been published within this topic receiving 2028987 citations. The topic is also known as: computer software & computational tool.
Papers published on a yearly basis
Papers
More filters
01 Jan 2001
4,604 citations
TL;DR: Calibration methods and software have been developed for single crystal diffraction experiments, using both approaches for calibrate, and apply corrections, to obtain accurate angle and intensity information.
Abstract: Detector systems introduce distortions into acquired data. To obtain accurate angle and intensity information, it is necessary to calibrate, and apply corrections. Intensity non-linearity, spatial distortion, and non-uniformity of intensity response, are the primary considerations. It is better to account for the distortions within scientific analysis software, but often it is more practical to correct the distortions to produce ‘idealised’ data. Calibration methods and software have been developed for single crystal diffraction experiments, using both approaches. For powder diffraction experiments the additional task of converting a two-dimensional image to a one-dimensional spectrum is used to allow Rietveld analysis. This task may be combined with distortion correction to produce intensity information and error estimates. High-pressure experiments can introduce additional complications and place new demands on software. Flexibility is needed to be able to integrate different angular regions se...
4,426 citations
TL;DR: PTRAJ and its successor CPPTRAJ are described, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions and the data therein derived.
Abstract: We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambe...
4,382 citations
Book•
18 Feb 1993
TL;DR: In this paper, the authors present a set of programs that summarize data with histograms and other graphics, calculate measures of spatial continuity, provide smooth least-squares-type maps, and perform stochastic spatial simulation.
Abstract: Thirty-seven programs that summarize data with histograms and other graphics, calculate measures of spatial continuity, provide smooth least-squares-type maps, and perform stochastic spatial simulation.
4,301 citations
TL;DR: A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is developed, which will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer.
Abstract: Structural genomics seeks to expand rapidly the number of protein structures in order to extract the maximum amount of information from genomic sequence databases. The advent of several large-scale projects worldwide leads to many new challenges in the field of crystallographic macromolecular structure determination. A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is therefore being developed. This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer.
4,201 citations