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RIKEN Harima Institute




Domestic Lab.

ĹѲʳ 渦漼
̳ƻ ιʬҲϳعֺ裲 (淮漼)

Program Search

SINCRIS software list

Intensity Integration of Diffraction image

DPS : free, No license

The Data Processing Suite (DPS) will be a complete package for processing of single crystal X-ray diffraction data of proteins, viruses, nucleic acids and other large biological complexes. The emphasis is on data collected at synchrotron sources. DPS is a collaboration between ADSC, and Cornell and Purdue universities.

MOSFLM : free, No license

This describes MOSFLM version 6 for processing image plate and CCD data (Progrum download)

HKL2000 : $0 or $1,500 or ...

HKL Research, Inc. provides high quality software and hardware solutions for X-ray crystallography laboratories and synchrotron beam lines. Our products have been used by over 800 groups and laboratories worldwide, including over 70 leading pharmaceutical companies. The software distributed by us is available at 62 synchrotron beam lines.

XDS : free, No license

Daresbury Laboratory Laue Software Suite (LAUEGEN, NEWLAUE, GENLAUE, etc.) : free, No license

Phase Determination

CCP4 : free

XtalView : free, No license

XTALVIEW is a package for X-ray crystal structure solution from the point at which data is collected through the fitting of a molecular model into an electron density map. XtalView runs on ordinary workstations and does not require 3-D hardware.

SHELX : free, site license (by e-mail)

SHELX is a set of programs for crystal structure determination from single-crystal diffraction data. SHELXS - Structure solution by Patterson and direct methods
SHELXL - Structure refinement (the version SHELXH is for large structures)

Shake and Bake (SnB) : free, site license (by WWW)

A direct-methods procedure for determining crystal structures.

Solve : $500+$100 x (sites num.), site license (by WWW)

Automated structure solution for MIR and MAD

SHARP : free, Site license (On line)

SHARP is a Statistical Heavy Atom Refinement and Phasing program. It operates on reduced, merged and scaled data from SIR(AS), MIR(AS) and MAD experiments, refines the heavy-atom model, helps detect minor or disordered sites using likelihood-based residual maps, and calculates phase probability distributions for all reflexions in the dataset.

BUSTER : free, Site license (On line)

A program for recovering missing phase information by Bayesian inference.

Molecular Building (refinement)

X-PLOR : $350, each licenses (by e-mail)

CNS : free, one license (by WWW)

TNT : free (?), each licenses (by letters)

ARP/wARP : free, site license (by WWW)

ARP/wARP is used for the refinement of protein structures via automatic updating and re-building of the model and solvent structure.

Molecular Building (Graphics)

O : free, each licenses (by e-mail)

Coot : free, No licenses

MI-fit : free, each licenses

Uppsala Software Factory : free, No licenses

TURBO FRODO : unkown, each licenses (by e-mail)

Presentation (Draw image of Protein Strutctre)

GRASP : $500, site license (by WWW)

MolScript : free, site license (by WWW)

Povscript+ : free, site license (by e-mail)

Raster3D : free, No licenses


RasMol : free, No licenses

VRML : free, No licenses

Flex : free, No licenses

Flex is a simple display program that can show molecules and animation sequences from disk files or from network connections to running programs -- for example, a molecular dynamics simulation. A library of communication routines is included which makes it very simple to add this real-time display ability to any program.

Shape : free, obtain license (by WWW)

Shape is a package for analysis of molecular surfaces. It includes programs for determining whether a point is in a groove or crevice in a surface, and for determining the largest sphere that can fit at a location.

WPD : free, No license

WPDB (the Protein Data Bank through Microsoft Windows) is a PC based software package comprising a compressed version of all or parts of the PDB and a set of tools to query features of a single structure or perform a comparative analysis on multiple structures with emphasis on sequence alignment and structure superposition. WPDB is described in the paper by Shindyalov and Bourne, (1995) J. App. Cryst. 28(6) 847-852.

PDBtool : unknown

PDBtool is a UNIX based tool for browsing the features of a single macromolecular structure supplied in PDB format. PDBtool includes structure verification and limited query capabilities. PDBtool is currently in Beta Test. To be a tester contact Phil Bourne (

DOT : unknown

A software package for examining molecular interactions. DOT is new program for docking macromolecules to other molecules of any size. It runs efficiently on parallel systems ranging from networked workstations to supercomputers.

AMBER : unknown, obtain license (by e-mail)


Protein Structure Initiative (Structural Genomics)
X-ray WWW Server
International Union of Crystallography
Crystallography World Wide (IUCr)
MAD Phasing
X-ray Anomalous Scattering
Crystallography Software
Symmetry Equivalent Positions Generator
Periodic Table of Elements
National Nuclear Data Center (BNL)
Physical Reference Data (NIST)
X-ray attenuation length
X-ray transmission of solid
Protein Data Bank (Osaka Univ. Mirror)
Cambridge Crystallographic Data Centre
SCOP(BERI mirror)
NCBI (Entrez, PubMed, VAST etc.)
Annual Reviews
NIST Crystal Data