Tasks page
This is a list of the Tasks PAN Blend is made of:
Table of contents
This metapackage will install PAN Blend coherent diffraction packages.
Debian packages in New queue (hopefully available soon)
-
Pynx
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Python tools for Nano-structures Crystallography (Scripts)
No known packages available
-
Bonsu
-
phase retrieval software package for real-time visualisation
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Hawk
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diffraction pattern reconstruction
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Ptypy
-
Ptychography Reconstruction for Python
This metapackage will install Debian PAN packages related to control
systems acquisition used in the PAN facilities.
Official Debian packages with high relevance
-
Ghkl
-
diffractometer computation control application
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Python3-sardana
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instrument control and data acquisition system - library
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Python3-tango
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API for the TANGO control system (Python 3)
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Python3-taurus
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Framework for scientific/industrial CLIs and GUIs - Python3
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Python3-taurus-pyqtgraph
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Taurus extension providing pyqtgraph-based widgets (Python 3)
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Tango-accesscontrol
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TANGO distributed control system - accesscontrol server
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Tango-db
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TANGO distributed control system - database server
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Tango-starter
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TANGO distributed control system - starter server
Packaging has started and developers might try the packaging code in VCS
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Micromanager
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Microscopy Software
No known packages available
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Opengda
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framework for creating customised data acquisition software for science
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Tomographie-preexperiment-data-collector
-
gather all information from the user that can be
This metapackage will install Debian PAN packages which might be
helpful for development of applications related to control system
acquisition.
You might also be interested in the control-system metapackage.
Official Debian packages with high relevance
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Libhkl-dev
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diffractometer computation control library - development files
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Libtango-dev
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TANGO distributed control system - development library
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Python3-sardana
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instrument control and data acquisition system - library
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Python3-tango
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API for the TANGO control system (Python 3)
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Python3-taurus
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Framework for scientific/industrial CLIs and GUIs - Python3
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Python3-taurus-pyqtgraph
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Taurus extension providing pyqtgraph-based widgets (Python 3)
No known packages available
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Libuca
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generic solution to access two-dimensional detectors
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Lima
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Library for Image Acquisition
This metapackage will install framework dedicated to the data reduction
Official Debian packages with high relevance
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Fityk
-
general-purpose nonlinear curve fitting and data analysis
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Gnuplot
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Command-line driven interactive plotting program.
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Imagej
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Image processing program with a focus on microscopy images
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Libxy-bin
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xylib - utilities
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Ngraph-gtk
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create scientific 2-dimensional graphs
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Octave
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GNU Octave language for numerical computations
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Pymca
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Applications and toolkit for X-ray fluorescence analysis -- scripts
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Scilab
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Scientific software package for numerical computations
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Silx
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Toolbox for X-Ray data analysis - Executables
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Spyder3
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Python IDE for scientists
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Vistrails
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Science visualisation workflow toolkit
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Xmaxima
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Computer algebra system -- x interface
No known packages available but some record of interest (WNPP bug)
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Thredds
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The THREDDS Data Server (TDS) is a web server that
No known packages available
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Dawn
-
general purpose data acquisition and processing
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Disp
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Diffraction Image Statistics Package for R
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Edna
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Framework to build online data analysis programs
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Graphlab
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A New Parallel Framework for Machine Learning
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Gumtree
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general purpose data acq and processing
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Mantid
-
?
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Nexpy
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A Python GUI to analyze NeXus data
This metapackage will install all PAN Blend packages. This is
a temporary package until we sorted all packages into the right
categories.
Official Debian packages with high relevance
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Libmgl-dev
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library for scientific graphs (development files)
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Libnexus-dev
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NeXus scientific data file format - development libraries
No known packages available
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Cdma
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Common Data Model API
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Comete
-
widget toolkit
This metapackage will install all diffraction softwares
Official Debian packages with high relevance
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Binoculars
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Surface X-ray diffraction 2D detector data reduction
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Xrayutilities
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transitional package
Official Debian packages with lower relevance
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Nebula
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performant, scalable network overlay
This metapackage will install all GID, GIXD, GIND, GISAS, GISAXS, GISANS softwares
Official Debian packages with high relevance
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Xrayutilities
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transitional package
No known packages available
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Fitgisaxs
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?
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Gsas
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?
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Isgisaxs
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gisaxs -- diffraction
This metapackage will install all laue saoftwares
No known packages available
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Esmeralda
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Esmeralda Laue Suite
This metapackage will install all microscopy softwares.
Official Debian packages with high relevance
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Gwyddion
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Scanning Probe Microscopy visualization and analysis tool
Official Debian packages with lower relevance
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Threeb
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3B Microscopy Analysis Software - command-line tool
This metapackage will install all MX diffraction softwares.
Official Debian packages with high relevance
-
Apbs
-
Adaptive Poisson Boltzmann Solver
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Autodock
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analysis of ligand binding to protein structure
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Clustalw
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global multiple nucleotide or peptide sequence alignment
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Gnuplot
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Command-line driven interactive plotting program.
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Imagej
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Image processing program with a focus on microscopy images
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Jmol
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Molecular Viewer
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Libmmdb2-0
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macromolecular coordinate library - runtime
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Openbabel
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Chemical toolbox utilities (cli)
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Povray
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Persistence of vision raytracer (3D renderer)
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Pymol
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Molecular Graphics System
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Python
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interactive high-level object-oriented language (Python2 version)
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Rasmol
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visualization of biological macromolecules
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Raster3d
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tools for generating images of proteins or other molecules
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Theseus
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superimpose macromolecules using maximum likelihood
Official Debian packages with lower relevance
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Dials
-
Diffraction Integration for Advanced Light Sources
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Gemmi
-
library for structural biology - executable
Debian packages in contrib or non-free
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Powder
-
Graphical dungeon crawling game
Debian packages in New queue (hopefully available soon)
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Coot
-
model building program for macromolecular crystallography
Packaging has started and developers might try the packaging code in VCS
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Cctbx
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CCTBX is a toolbox for developing crystallographic
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Crystfel
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Suite of programs for processing "serial" diffraction data "snapshots"
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Nmoldyn
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?
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Rosetta
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molecular biophysics for structural biology
Unofficial packages built by somebody else
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Evrouter
-
?
No known packages available
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3dna
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3DNA is a versatile, integrated software system for
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Adxv
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The principal application of adxv is to display
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Aimless
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This program scales together multiple observations of
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Albula
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Dectris diffraction image viewer and analysis tool
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Aplx
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?
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Atsas
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?
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Autoproc
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MX data processing
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Balbes
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BALBES is a system for solving protein structures
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Best
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optimal planning of X-ray data collection from protein crystals
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Biox-xds
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?
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Bioxhit
-
?
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Bobscript
-
?
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Bp3-old
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?
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C3d
-
?
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Cath
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CATH is a manually curated classification of protein
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Ccp4
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CCP4 exists to produce and support a world-leading,
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Chart
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?
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Chimera
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UCSF Chimera is a highly extensible program for
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Chooch
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CHOOCH is a program that will automatically determine
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Cn2coot
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?
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Cns
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Crystallography & NMR System (CNS) is the result of
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Crank
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Crank [1] is a program to automate macromolecular
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Das
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The Distributed Annotation System (DAS) defines a
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Dna
-
?
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Domain-finder
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DomainFinder is an interactive program for the
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Dps2ar
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The EMBL-Hamburg automated crystal structure
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Dviewer
-
?
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Dyndom3d
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DynDom3D is a new program for the analysis of domain
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Edna
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Framework to build online data analysis programs
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Edna
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EDNA is a framework for developing plugin-based
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Elves
-
?
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Epmr
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EPMR is a general-purpose molecular replacement
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Escet
-
?
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Fit2d
-
?
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Fobscom
-
?
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Gramm
-
?
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Grasp
-
?
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Harker
-
?
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Hbplus
-
?
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Hca
-
?
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Hkl2map
-
?
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Hyss
-
?
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Imosflm
-
?
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Induced-rad-dam
-
?
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Ipymol
-
?
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Ispyb-client
-
?
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Labelit
-
?
-
Lam
-
?
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Laue
-
?
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Liged
-
?
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Ligplot
-
?
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Ligplus
-
?
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Lscale
-
?
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Maid
-
?
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Main
-
?
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Mar345
-
?
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Marutils
-
?
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Mercury
-
?
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Mlfsom
-
?
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Molscriptmolscript-2.1.2
-
?
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Mosflm
-
?
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Msi
-
?
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Nuccyl
-
?
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Nucplot
-
?
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Onoono80ono90
-
?
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Phaser
-
?
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Phases
-
?
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Phenix
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automated determination of macromolecular structures
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Phenix
-
?
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Pirate
-
?
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Plotmtv
-
?
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Pointless
-
?
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Promotif
-
?
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Pxpy
-
?
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Raddose
-
?
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Refmac
-
?
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Replace
-
?
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Ribbons
-
?
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Ringer
-
?
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Rmerge
-
?
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Rtools
-
?
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Saxs
-
?
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Shakerr
-
?
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Sharp
-
?
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Shelx
-
?SHELX is a set of programs for crystal structure
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Sir
-
?
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Sir2002
-
?
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Snb2.2
-
?
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Snow
-
?
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Solvesolve-2.08
-
?
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Stac-stac2
-
?
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Strategy
-
?
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Surfnet
-
?
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Tcltkblt
-
?
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Testcase
-
?
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Textal
-
?
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Tools
-
?
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Tops
-
?
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Usf
-
?
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Viewhkl
-
?
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Wink
-
?
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Workflow-ds
-
?
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Workflow-executor
-
?
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Xds
-
?
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Xdsme
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XDS Made Easier
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Xiaxia2
-
?
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Xprep
-
?
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Xrec
-
?
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Xtalview
-
?
This metapackage will install Debian PAN packages which might be
helpful for development of applications related to Macro-Molecular
diffraction.
You might also be interested in the mx metapackage.
Official Debian packages with lower relevance
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Libccp4-dev
-
CCP4 core functionality - development files
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Libclipper-dev
-
object oriented development kit for crystallographic computing
-
Libmmdb-dev
-
macromolecular coordinate library - development files
-
Libssm-dev
-
macromolecular superposition library - development files
Packaging has started and developers might try the packaging code in VCS
-
Libccif-dev
-
<insert up to 60 chars description>
This metapackage will install all powder diffraction softwares.
Official Debian packages with high relevance
-
Fityk
-
general-purpose nonlinear curve fitting and data analysis
-
Libxy-bin
-
xylib - utilities
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Objcryst-fox
-
Free Objects for Xtallography
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Pyfai
-
Fast Azimuthal Integration scripts
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Spd
-
Synchrotron image corrections and azimuthal integration
No known packages available
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Fullprof
-
?
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Jpowder
-
Lightweight powder diffraction data visualizer
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Pygsas
-
crystallography multi purpose python library
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Pyxrd
-
matrix algorithm for X-ray diffraction patterns
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Xrdua
-
X-ray Powder Diffraction
This metapackage will install all PAN Blend small angle scattering.
Official Debian packages with high relevance
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Fityk
-
general-purpose nonlinear curve fitting and data analysis
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Pyfai
-
Fast Azimuthal Integration scripts
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Sasview
-
Small Angle Scattering Analysis suite
-
Spd
-
Synchrotron image corrections and azimuthal integration
No known packages available
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Bsl
-
small angle scattering
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Diffraction-ring-profiler
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A program for extracting electron diffraction ring pattern profiles
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Sastbx
-
Small angle scattering
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Saxsview
-
?
This metapackage will install all spectroscopy software.
No known packages available
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Arpys
-
ARPES (Angle Resolved PhotoEmission Spectroscopy) data analysis
This metapackage will install all PAN Blend tomography packages.
Official Debian packages with high relevance
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Libufo-bin
-
Library for high-performance, GPU-based computing - tools
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Mayavi2
-
scientific visualization package for 2-D and 3-D data
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Paraview
-
Parallel Visualization Application
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Python3-skimage
-
Python 3 modules for image processing
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Ufo-filters
-
Set of plugins for ufo-core - runtime
Debian packages in contrib or non-free
-
Python3-pyhst2-cuda
-
Python High Speed Tomographic reconstruction
No known packages available
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Astra-toolbox
-
A high-performance GPU MATLAB toolbox for 2D and 3D tomography
-
Freeart
-
SART reconstruction algorithm
-
Imagej-pluggins-tomo
-
?
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Pyastra-toolbox
-
python binding for the astra-toolbox
-
Rabbitct
-
backprojection performance-comparison
-
Tomographie-preexperiment-data-collector
-
gather all information from the user that can be
-
Tomopy
-
tomographic data processing and image reconstruction toolbox
This metapackage will install all EXAFS and XANES softwares.
Official Debian packages with high relevance
-
Pymca
-
Applications and toolkit for X-ray fluorescence analysis -- scripts
-
Quantum-espresso
-
Electronic-Structure and Ab-Initio Molecular Dynamics Suite
Packaging has started and developers might try the packaging code in VCS
-
Xraylarch
-
X-ray Analysis for Synchrotron Applications using Python
No known packages available
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Prestopronto
-
Software for analysis of Quick Exafs data