Crystallographic software list

PARST96 Fortran program for the calculation of a variety of structural parameters from atomic coordinates, from X-ray, neutron, theoretical calculations etc.

PARVATI Validation/analysis tool for macromolecular structure refinements which include anisotropic displacement parameters (ADPs). Normally this means proteins refined at atomic or near-atomic resolution, using programs such as SHELX, REFMAC or RESTRAIN.

PASCal (Principal axis strain calculator) is designed to simplify the determination of principal coefficients of thermal expansion and compressibilities from variable-temperature and variable-pressure lattice parameter data.

PATE Extracts powder pattern information from GSAS files and outputs the observed, calculated, difference plots and reflection positions in a form that can be used by graphing software. It can handle multiple histograms (including time-of-flight) and multiple phases.

PATGEN An automatic program to generate theoretical Patterson peaks and to compare them with experimental peaks

PATSEE Structure solution program. Location of a fragment of known geometry by integrated Patterson, packing, and direct methods

PATTERN This is a program to plot a diffraction pattern from a dataset (any ascii format reflection file) on laserprinter, Silicon Graphics or ESV window by generating a postscript file. The picture is in a style of precession film.

PC Convolution educational software from Dr Kurt Kosbar kk@ee.umr.edu

PCMolecule Molecular graphics program used for displaying

PDB Program PDB is free software for the Macintosh for analysis of 3D

PDB-2-PB A curated online protein block sequence database. PDB-2-PB version 1.0 has the curated protein block sequences for 103 252 PDB chain entries (93 547 X-ray, 7033 NMR and 2672 other experimental chain entries).

PDB2VRML PDB to VRML converter for 3D examination of

Pdb-lib.pl Perl library for reading and writing PDB format coordinate files. The PdbRead subroutine is hacked/translated from the CCP4 fortran library PDBREAD (in RWBROOK.F). It's useful for writing perl jiffies. For further information contact Charlie Bond

PDBTool PDB to VRML converter for 3D examination of

PDFFIT Full profile structural refinement of the atomic pair distribution function (PDF). Allows the refinement of multiple data sets and/or structural phases. Provides a complimentary tool to traditional Rietveld by probing the local rather than long range structure of a material.

PDFgetN Data analysis package used to generate pair distributions functions (PDF's) using neutron powder diffraction data collected at neutron spallation sources

PDFgetX Computation of the pair distribution function (PDF) from X-ray powder diffraction data. Gives the total scattering structure function, S(Q), from the X-ray powder diffraction data by applying corrections for experimental effects such as multiple scattering, absorption, polarization effects and Compton scattering.

PDFgetX3 A new software application for converting X-ray powder diffraction data to an atomic pair distribution function (PDF). In comparison to the preceding programs, PDFgetX3 requires fewer inputs and less user experience and it can be readily adopted by novice users.

pdfgui Software for fitting local and intermediate structures to atomic pair distribution functions (PDFs) obtained from x-ray and neutron diffraction data. Please see the entry for PDFgui (respecting capitalization) for more details.

PDFgui For modeling of local structure and nanostructure in materials from atomic pair distribution functions (PDFs). This is a refinement program that takes an initial structure, in the form of a crystal structure, for example from a cif file, and refines structural parameters by fitting to PDF data from x-ray or neutron diffraction experiments. It has an easy to use graphical user interface.

Peaksplit Analysis of pairs of rocking curves to give strain, relaxation, and composition information for ternary alloy layers. Developed by Bede Scientific.

Pentacle On-line calculation of Fourier transforms. Allows EM operator to see the image and the FT on the same screen.

Pepinsky's Machine Both a teaching aid to illustrate the principles and the application of the Fourier series in crystallography, and a research tool to permit the systematic calculation of permutation syntheses for all centrosymmetric plane groups

PGplot Plotting program

PHENIX A new Python-based graphical user interface for the PHENIX suite of crystallography software.

PhIdo Use of diffraction patterns for chemical identification

Photon Scattering Software Photon Scattering Software

Piotr Marczuk reflectivity calculator GUI to calculate the neutron or x-ray reflectivity from a (repetitive) multilayered sample, i.e. a Langmuir-Blodgett film.

PITRE Software for Phase-sensitive X-ray Image processing and Tomography REconstruction written in IDL.

PKFIT Peak fitting, see CCP14

Plasmid Draw vector maps and perform DNA sequence analysis. Integrated web browser and ability to instantly convert sequence files from the Internet into fully labeled graphical maps.

Plasmid Processor Tool for plasmid presentation for scientific and educational purposes

PLATON Versatile SHELX97 compatible multipurpose crystallographic tool implementing the following features: standard geometrical calculations, descriptors, tests, utilities, graphics

Point Group Tutorial Multimedia program designed to help students identify symmetry elements and assign point groups to molecules. Includes example molecules for each point group and an interactive tutorial based on the traditional flow-chart method for assigning point groups.

Polaber A program for the calculation and visualization of distributed atomic polarizabilities, quantities which are useful for the evaluation of crystal properties such as the optical indicatrix.

PolySNAP A program that automatically classifies and clusters structural fragments extracted from mining the Cambridge Structural Database. See dSNAP

PorphyStruct PorphyStruct, a new digital tool for the analysis of non-planar distortion modes of different porphyrinoids - The program makes use of the normal-coordinate structure decomposition technique (NSD) and employs sets of normal modes equivalent to those established for porphyrins in order to describe the out-of-plane dislocation pattern of perimeter atoms from corroles, norcorroles, porphycenes and other porphyrinoids quantitatively and in analogy to the established terminology.

POTATO Generation of Perovskite Structures distorted by tilting of rigid octahedra

Powder3D A multi-pattern data reduction and graphical presentation software

Powder Cell Displays crystal structures, uses different data formats. The aim of this program is the intuitive generation of initial structure models to use them in refinement procedures, e.g. in so called Rietveld programs.

Powder Diffraction Powder Diffraction Programs (World Directory of).

POWDER/PWCDS Indexation of Debye-Scherrer Powder diagrams

PowderV2 Suite of applications designed to ease the treatment of X-ray powder diffraction. Development of the earlier program Convert for Windows.

PowderX Graphical display of the diffraction pattern, smoothing, K-alpha2 elimination, background strip, peak search, automatic correction of the zero-angle error, indexing of the Powder x patterns and data format conversion prepare data files for EXPO, DBWS, FULLPROF, GSAS, SIMPRO programs and much more. Zip files can be downloaded off the web and password for extracting the ZIP files obtained by E-mailing the author: Cheng Dong (chengdon@aphy.iphy.ac.cn)

POWDIS-POWUTL Display and simulation of powder patterns

PowDLL PowDLL is a .NET dynamic link library used for the interconversion procedure between variable formats of Powder X-Ray files. The DLL is capable of handling the most common file formats (binary and ASCII). The library can be used as a reusable component with any .NET language. It is distributed with PowDLL converter which is the front-end application that can convert most of the known powder diffraction file types.

Powf :A program to convert powder diffraction datafile formats

PREMOS91/REMOS Programs for modulated structures. REMOS: least-squares program for the refinement of modulated structures for a single crystal. PREMOS: the powder version of REMOS. MODPLT: a program for plotting modulation functions. PRJMS: a program for plotting modulated structure in 3D space.

PREPI PREPI is a molecular graphics program which can be used to EASILY produce and interactively manipulate many different types of molecular representations (cartoons) as well as providing quantative information on secondary structural topology.

PreQuest A database building program whose primary objective is to create high quality structural data files in a format searchable by ConQuest.

Primer PrimerDesign is a DOS-program to choose primer for PCR or oligonucleotide probes. It is tailored to check known sequences for repeats and unique sequences and subsequently to create prober primers according to this data.

PRIMUS Perfoms manipulations with experimental small-angle scattering data files such as: averaging, subtraction, merging, extrapolation to zero concentration and curve fitting and evaluates the integral parameters from Guinier and Porod plots such as radius of gyration

PRJMS Yamamoto's program for plotting modulated structure in 3D space.

ProAnWin Multiple protein

ProcessDiffraction To process electron diffraction patterns from polycrystalline or amorphous samples.

processPIXEL A program to generate energy-vector models from Gavezzotti's PIXEL calculations.

PROCHECK PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure.

PROCHEMIST Modeling package. Includes Molecular Mechanics(MMX)and Semi-emprical(Mopac 6.0) for geometry optimization,conformationnal research(using recent techniques as genetic algorithms),Lipophicity calcs(Logp..),Qsar and datamining(Factorial analysis,neuronal network&genetic algorithm)

Procreate Protein visualisation tool. Aims to provide a powerful, extensible environment in which users can easily customise the program to view the data exactly how they want

Profex Profex is a graphical user interface for Rietveld refinement of powder X-ray diffraction (XRD) data with the Rietveld kernel BGMN. It can be used for phase identification, phase quantification, structure refinement, generation of electron density maps and waterfall plots, generic peak fitting, peak integration, file conversion, and export of results and graphs to tables and figures. The program supports a variety of raw data file formats and can import structural data from CIF and ICDD XML files. Profex and BGMN are distributed as free and open-source software and run on Windows, MacOS and Linux.

PROFIL Rietveld method. For further information contact CCP14 or contact J. K. Cockcroft.

ProFIT Protein Fold Identification Tool. Combines an aminoacid sequence

PROFITVZ GUI programm for X-ray and neutron powder data treatment. Peak fitting. Overlapping reflections. Permits to process total pattern part by part. DOS and WINDOWS operating systems.

PROFVAL Functions to calculate powder-pattern peak profiles with axial-divergence asymmetry.

ProMSED2 ProMSED2 is the enhancement of ProMSED made according to user's remarks and suggestions.

PROSA Aimed at the determination of a protein's native fold. Assists you in protein structure quality control. It calculates a score for your input-structure. Scores of native protein folds are in a characteristic range.

PROSPERO The PROSPERO web server is intended both to provide a means of organizing the potentially large numbers of experimental characterizations measured from purified proteins, and to provide useful guidance for structural biologists who have succeeded in purifying their target protein but have reached an impasse in the difficult and poorly understood process of turning purified protein into well diffracting crystals.

PROSZKI Set of popular programs for powder diffraction data analysis: PRMAIN maintains data files and prepares input files, APPLE refinement of unit cell parameters, DICVOL indexing, LATCON refinement of unit cell parameters, LAZY diffraction pattern simulation, NEWPEAK diffraction pattern analysis, POWDER, TREOR,VISSER indexing.

PROTEIN Integrated collection of crystallographic programs designed for the structure analysis of macromolecules.

ProtRot Uses quaternions to calculate the best superposition of molecule models in pdb format

PSA Protein Sequence Analysis

PSAP A web based suite for protein structure analysis. Calculate and display various hidden structural and functional features of three-dimensional protein structures.

PSdbView Java based vizualization tool for viewing PSdb entries. The

PSILAM Calculation and graphical representation of multiple diffraction patterns (intensity dependent psi-lambda peak location plot). Version 01.01

PTCLab PTCLab is an abbreviation of phase transformation crystallography lab. The purpose of this program is to calculate the transformation crystallography after a phase transformation and represent the results in graphical way such as in stereo graphic projection. The lattice matching near the interface, the superimposed diffraction patterns and so on can be readily simulated with present program. This program is free, opensource and runnable on multiple platform.

PTCLab-EBSD Now new EBSD module for PTCLab which can simulate EBSD pattern, view EBSD data, and for variant selection analysis.

publCIF publCIF takes a crystallographic information file (CIF) and prepares a formatted paper (Preprint) in the style of Acta Crystallographica Sections C and E, and IUCrData.

PULWIN2 Analysis of powder diffraction patterns. Allows cell refinement, peak search and indexing, background estimation, peak fitting. Allows also the use of diffractograms collected with CPS 120 detectors. A calibration procedure is available to convert "channel" units into "2-theta" units.

PyCogent New functionality for three-dimensional structure processing and analysis has been introduced into PyCogent - a popular feature-rich framework for sequence-based bioinformatics, but one which has lacked equally powerful tools for handling stuctural/coordinate-based data

pyEBSD pyEBSD is a free and open-source software to post-process Electron Backscatter Diffraction (EBSD) data, inducing IPF mapping, image quality mapping, phase mapping etc, plotting pole figure, data segmentation, statistic analysis of the misorientation distribution etc. The software is written by python, and it supports both script and graphic user interface.

pyFAI PyFAI is an azimuthal integration library that tries to be fast (as fast as C and even more using OpenCL and GPU). It is based on histogramming of the 2theta/Q positions of each (center of) pixel weighted by the intensity of each pixel, but parallel version uses a SparseMatrix-DenseVector multiplication. Neighboring output bins get also a contribution of pixels next to the border thanks to pixel splitting. Finally pyFAI provides also tools to calibrate the experimental setup using Debye-Scherrer rings of a reference compound.

PyMOL PyMOL is a user-sponsored molecular visualization system on an open-source foundation. Please support development of this open, effective, and affordable software by purchasing an incentive copy, which is pre-built and comes with maintenance and support.

PyNX An open-source software toolbox (PyNX) is presented, with a few examples showing the fast calculation of scattering maps from strained nanostructures, including grazing-incidence conditions.