PAN Blend mx packages

APBS est un paquet pour la résolution numérique de l'équation de Poisson-Boltzmann (PBE), un des modèles continus les plus populaires décrivant les interactions entre solutés moléculaires en milieu aqueux et salin. Le continuum électrostatique joue un rôle important dans plusieurs domaines de la simulation biomoléculaire, incluant :

 – la simulation des processus de diffusion pour déterminer les cinétiques
    de liaison ligand-protéine et protéine-protéine ;
 – la dynamique moléculaire de solvatation des biomolécules ;
 – le calcul de l'énergie de solvatation et de liaison pour déterminer
   les constantes d'équilibre de liaison ligand-protéine et
   protéine-protéine afin d'aider à la conception rationnelle de
   médicaments ;
 – les études de titration biomoléculaire.

APBS est conçu pour évaluer efficacement les propriétés électrostatiques pour de telles simulations dans un large spectre d'échelles de longueur pour permettre l'étude de molécules de dix à des millions d'atomes.

Ce paquet fournit de programme apbs et des utilitaires.

Autodock est un des programmes principaux d'amarrage moléculaire (docking) de ligands de faible poids moléculaire à des récepteurs protéiques. Dans les versions précédentes le ligand était complètement flexible tandis que la protéine était rigide. La version 4 permet de considérer la protéine de manière partiellement flexible pour les chaînes latérales de résidus de surface sélectionnés en prenant en compte les rotamères.

Le programme AutoDock réalise l'amarrage moléculaire de ligands en utilisant des grilles pré-calculées qui décrivent la protéine cible en terme de préférence spatiale physico-chimique. AutoGrid pré-calcule ces grilles.

Ce programme réalise l'alignement de séquences multiples de nucléotides ou d'acides aminés. Il identifie le format des séquences en entrée et détermine s'il s'agit d'acides nucléiques (ADN/ARN) ou d'acides aminés (peptides). Le format en sortie peut être choisi parmi divers formats pour les alignements multiples, comme Phylip ou FASTA. Clustal W est largement reconnu.

Les données en sortie de Clustal W peuvent être modifiées manuellement ou avec un éditeur d'alignement comme Seaview ou le logiciel compagnon Clustal X. Lorsqu'un modèle est construit à partir des alignements, il peut être utilisé pour améliorer les recherches dans les bases de données. Celles-ci peuvent être créées sous forme de modèles de Markov (HMM) avec le paquet HMMER.

The DIALS software is developed in a fully open-source, collaborative environment. The main development teams are based at Diamond Light Source and CCP4, in the UK, and at Lawrence Berkeley National Laboratory, USA. However, in the spirit of the open source movement, we welcome collaboration from anyone who wishes to contribute to the project.

To avoid “reinventing the wheel” as much as possible, the DIALS project builds on knowledge accumulated over many decades in the field of crystallographic data processing. We benefit greatly from the altruism of experts who contribute their ideas and advice, either directly or via their detailed publications on existing algorithms and packages such as XDS [2] and MOSFLM [3]. At the heart of the DIALS framework lies a design philosophy of hardware abstraction and a generalised model of the experiment that is inspired directly by material published on the seminal workshops on position sensitive detector software [1]. Continuing in the spirit of these workshops we held our own series of meetings, with talks from invited speakers, and code camps in which specific problems are addressed by intensive effort across the collaboration. Summaries of these meetings and copies of slides given as presentations are available here.

DIALS is written using Python and C++, making heavy use of the cctbx [4] for core crystallographic calculations and much infrastructure including a complete build system. Seamless interaction between the C++ and Python components of this hybrid system is enabled by Boost.Python. Python provides a useful ground for rapid prototyping, after which core algorithms and data structures may be transferred over to C++ for speed. High level interfaces of the hybrid system remain in Python, facilitating further development and code reuse both within DIALS and by third parties.

Gnuplot est un utilitaire de tracé de données et de fonctions en ligne de commande qui prend en charge de nombreux formats de sortie, dont les pilotes pour de nombreuses imprimantes, (La)Tex, (x)fig, Postscript, etc. La version X11 est empaquetée dans gnuplot-x11.

Les fichiers de données et les fonctions définies par l'utilisateur peuvent être manipulés avec le langage interne de gnuplot (type langage C). Gnuplot peut effectuer des lissages, des régressions linéaires ou non linéaires (par splines notamment) et peut travailler avec les nombres complexes.

Ce métapaquet permet d’installer gnuplot avec toutes ses possibilités (-qt, -x11 ou -nox).

Ce programme peut afficher, éditer, analyser, traiter, enregistrer et imprimer des images 8, 16 et 32 bits. Il peut lire de nombreux formats d'image, dont TIFF, GIF, JPEG, BMP, DICOM, FITS et RAW. Il prend en charge les « stacks », une série d'images partageant une même fenêtre.

ImageJ peut calculer des statistiques de zones et pixels à partir de sélections de l'utilisateur. Il peut mesurer les distances et les angles. Il peut créer des histogrammes de densité et des affichages de profils linéaires. Il prend en charge les fonctions standard de traitement d'images telles que la manipulation du contraste, l'accentuation, l'adoucissement, la détection d'arêtes et le filtrage médian.

La calibration spatiale est disponible pour fournir des mesures de dimensions réelles dans des unités comme le millimètre. La calibration de la densité ou des niveaux de gris est également disponible.

ImageJ est développé par Wayne Rasband (wayne@codon.nih.gov) dans la Research Services Branch du National Institute of Mental Health à Bethesda, Maryland, USA.

Jmol est un visualisateur Java moléculaire pour des structures chimiques en trois dimensions. Ses fonctions comprennent la lecture d’une variété de types de fichiers et de sorties de programmes de chimie quantique, l’animation de fichiers de multi-trames et les modes normaux calculés à partir de programmes quantiques. Il englobe des fonctions pour les produits chimiques, les cristaux, les matériaux et les biomolécules. Jmol peut être utile pour des étudiants, des enseignants ou des chercheurs en chimie et biochimie.

Les formats lus par Jmol comprennent PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton et VASP.

MMDB is designed to assist developers in working with macromolecular coordinate files. The library handles both PDB and mmCIF format files.

The Library also features an internal binary format, portable between different platforms. This is achieved at uniformity of the Library's interface functions, so there is no difference in handling different formats.

MMDB provides various high-level tools for working with coordinate files, including reading and writing, orthogonal-fractional transforms, generation of symmetry mates, editing the molecular structure and more.

This package contains the shared library components needed for programs that have been linked to the mmdb library.

Open Babel est une boite à outils dans le domaine de la chimie. Elle a été conçue pour prendre en charge les nombreux langages des données chimiques. Elle permet de rechercher, convertir, analyser ou bien stocker les données de modélisation moléculaire, de chimie, de matériaux solides, de biochimie ou de domaines connexes. Les fonctionnalités comprennent :

 − ajout ou suppression d'hydrogène ;
 − gestion de la dynamique moléculaire ;
 − gestion de la syntaxe de reconnaissance moléculaire SMARTS ;
 − perception automatique des propriétés (cycles, liaisons,
    hybridation ou aromaticité) ;
 − typage flexible des atomes et perception des liaisons multiples
    d'après les coordonnées atomiques ;
 − calcul de charge partielle de Gasteiger-Marsili.

Les formats de fichiers traités par Open Babel comprennent : PDB, XYZ, CIF, CML, SMILES, MDL, Molfile, ChemDraw, Gaussian, GAMESS, MOPAC et MPQC.

Ce paquet comprend les utilitaires suivants :

 – obabel : conversion entre divers formats de fichiers de chimie ;
 – obenergy : calcul de l'énergie d'une molécule ;
 – obminimize : optimisation de la géométrie, minimisation de l'énergie
                d'une molécule ;
 – obgrep : programme de recherche moléculaire utilisant le modèle
            SMARTS ;
 – obgen : génération des coordonnées en 3D d'une molécule ;
 – obprop : affichage des propriétés standard d'une molécule ;
 – obfit : superposition de deux molécules à partir d'un modèle ;
 – obrotamer : génération de coordonnées de conformères ou rotamères ;
 – obconformer : génération de conformères de faible énergie ;
 – obchiral : affichage des informations de chiralité moléculaire ;
 – obrotate : notation d’angle dièdre de molécules en mode automatique
              (batch) ;
 – obprobe : création d’une grille de sonde électrostatique.

POV-Ray est un logiciel de lancer de rayons aux caractéristiques complètes. Le lancer de rayons simule des objets et des sources lumineuses du monde réel pour calculer des images réalistes à l’aide d’un ordinateur. Dû à la nature du tracé selon les rayons, ce processus est assez exigeant pour le processeur, pour bénéficier d’images plus réalistes en comparaison des techniques de rendu en temps réel. Par exemple, avec POV-Ray, il est possible de modéliser un prisme de verre et apercevoir le spectre dans l’image résultante.

POV-Ray en lui-même est un utilitaire en ligne de commande prenant une description de scène, écrite dans un langage spécial de compréhension aisée, pour produire des images de tracé par rayons (ou même des séquences d’images pour des animations). Ces descriptions peuvent être écrites à la main ou en utilisant des outils externes pour générer (des parties) de la scène.

Povray-includes est fortement recommandé en plus de ce paquet.

PyMOL est un programme de visualisation de molécules ciblant la biologie structurale pour des biomolécules moyennes ou grosses telles que les protéines. Il peut produire des graphismes et des animations de molécules de qualité professionnelle.

Les fonctions incluent :

 – la visualisation de molécules, de trajectoires moléculaires et de
   structures de données cristallographiques ou d’orbitales ;
 – un « constructeur » et « sculpteur » de molécules ;
 – un lanceur de rayons et un générateur de film internes ;
 – la possibilité de toutes extensions et scripts à l’aide d’une interface
   en Python.

Les formats de fichier que PyMOL peut lire incluent PDB, XYZ, CIF, MDL Molfile, ChemDraw, les « cartes » CCP4, XPLOR et Gaussian cube.

Il s’agit d’une boîte à outils logicielle pour la cristallographie qui fournit les modules suivants :

   – annlib_adaptbx,
   – boost_adaptbx,
   – cbflib_adaptbx,
   – ccp4io_adaptbx :enveloppes pour la fonctionnalité Boost dans CCTBX ;
   – cctbx : bibliothèques pour les applications de cristallographie,
             utiles pour la cristallographie de petites molécules et
             macro-molécules ;
   – cma_es,
   – crys3d : modules d’affichage de molécules, de densité d’électrons,
             et de données de réseau réciproque ;
   – dxtbx : la boîte à outils d’image de diffraction pour la gestion de
             détecteur de rayons X de complexité arbitraire pour
             différents formats standard ;
   – fable : bibliothèque d’émulation Fortran pour porter Fortran77 vers C++ ;
   – gltbx : liaisons de Python pour OpenGL ;
   – iotbx : travailler avec les formats courants de fichier de
             cristallographie ;
   – libtbx : le système de construction commun à tous les autres modules.
             Cela inclut une très fine enveloppe autour de l’outil
             logiciel de construction SCons. Il fournit aussi des
             utilitaires et des cadriciels utiles pour simplifier le
             développement d’application, incluant des outils de
             régression de test, la parallélisation à travers des systèmes
             multiprocesseurs et grappes et une syntaxe de configuration
             modulaire appelée PHIL (Python Hierarchial Interface Language)
             utilisée pour tout le CCTBX ;
   – mmtbx : fonctionnalité spécifique à la cristallographie de
             macro-molécules. Cela comprend toute la machinerie nécessaire
             pour le réglage des contraintes de géométrie, la correction
             et la mise à l’échelle de milieu ambiant, l’analyse de
             données de diffraction macro-moléculaire, le calcul de
             coefficients de mappage pondérés et la plupart des méthodes
             mises en œuvre dans phenix.refine. La majorité de
             l’infrastructure pour le serveur de validation MolProbity
             (et équivalent Phenix) est aussi située ici ;
   – omptbx : interface OpenMP ;
   – rstbx : boîte à outils de réseau réciproque pour autoindexer la
             diffraction de petites molécules Bragg, les vecteurs de
             de réseau réciproque indiqués ;
   – scitbx : calculs généraux scientifiques, incluant une famille de
             types de tableau C++ de haut niveau, une bibliothèque de
             transformée de Fourier rapide et un portage en C++ du
             minimiseur populaire L-BFGS quasi-Newton ;
   – smtbx : cristallographie de petites molécules ;
   – spotfinder :
   – tbxx :
   – wxtbx : contrôles wxPython utilisés dans l’interface graphique Phenix
             et utilitaires divers.

Ce paquet fournit une collection sélective de modules python du projet cctbx.

The DIALS software is developed in a fully open-source, collaborative environment. The main development teams are based at Diamond Light Source and CCP4, in the UK, and at Lawrence Berkeley National Laboratory, USA. However, in the spirit of the open source movement, we welcome collaboration from anyone who wishes to contribute to the project.

To avoid “reinventing the wheel” as much as possible, the DIALS project builds on knowledge accumulated over many decades in the field of crystallographic data processing. We benefit greatly from the altruism of experts who contribute their ideas and advice, either directly or via their detailed publications on existing algorithms and packages such as XDS [2] and MOSFLM [3]. At the heart of the DIALS framework lies a design philosophy of hardware abstraction and a generalised model of the experiment that is inspired directly by material published on the seminal workshops on position sensitive detector software [1]. Continuing in the spirit of these workshops we held our own series of meetings, with talks from invited speakers, and code camps in which specific problems are addressed by intensive effort across the collaboration. Summaries of these meetings and copies of slides given as presentations are available here.

DIALS is written using Python and C++, making heavy use of the cctbx [4] for core crystallographic calculations and much infrastructure including a complete build system. Seamless interaction between the C++ and Python components of this hybrid system is enabled by Boost.Python. Python provides a useful ground for rapid prototyping, after which core algorithms and data structures may be transferred over to C++ for speed. High level interfaces of the hybrid system remain in Python, facilitating further development and code reuse both within DIALS and by third parties.

This is the Python 3 version of the package.

Lightweight, simple Python(-only) package. It is used to provide access to data files used in regression tests, but does not contain any of those data files itself.

Although it is envisaged as mostly being used in a cctbx/DIALS environment for tests in DIALS, dxtbx, xia2 and related packages, it has no dependencies on either cctbx or DIALS, in fact all dependencies are explicitly declared in the setup.py file and are installable via standard setuptools/pip methods. This means dials_data can easily be used in other projects accessing the same data, and can be used in temporary environments such as Travis containers.

Python 3 tools for reading European XFEL's HDF5 files.

mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data.

It allows MRC files to be created and opened easily using a very simple API, which exposes the file's header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested.

This library aims to allow users and developers to read and write standard-compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions.

Key Features:

• Clean, simple API for access to MRC files
• Easy to install and use
• Validation of files according to the MRC2014 format
• Seamless support for gzip and bzip2 files
• Memory-mapped file option for fast random access to very large files
• Asynchronous opening option for background loading of multiple files
• Runs in Python 2 & 3, on Linux, Mac OS X and Windows

This package provides a neat and tidy Python interface for reading data from HDF5 files that are structured according to the NXmx application definition of the NeXus standard (https://www.nexusformat.org/).

RasMol est un programme graphique moléculaire destiné à la visualisation de protéines, d'acides nucléiques et de petites molécules. Le programme est destiné à l'affichage, l'apprentissage et la génération d'images de la qualité des publications.

Le programme lit un fichier de coordonnées de molécule et l'affiche interactivement à l'écran avec diverses couleurs et représentations. Les molécules chargées peuvent être montrées comme des structures filaires, des liaisons cylindriques (drieding), des sphères remplissant l'espace (CPK), des rubans macromoléculaires, des boules avec des liaisons, des rubans de biomoléculaires solides et en brins, des étiquettes d'atomes et des surfaces de points.

Sont actuellement pris en charge les formats Brookhaven Protein Databank (PDB), Tripos' Alchemy et Sybyl Mol2, les formats de fichiers Molecular Design Limited's (MDL) Mol, le format Minnesota Supercomputer Center's (MSC) XMol XYZ et les formats de fichiers CHARMm, CIF et mmCIF.

Ce paquet installe deux versions de RasMol : rasmol-gtk possède une interface moderne en GTK et rasmol-classic est la version avec l'ancienne interface graphique Xlib.

Raster3D est un ensemble d'outils pour la génération d'images matricielles de protéines ou d'autres molécules. Le logiciel principal rend les sphères, les triangles, les cylindres, les surfaces quadriques avec la surbrillance spéculaire, l'ombrage de Phong et l'ombrage. Il utilise l'algorithme efficace du logiciel Z-buffer, qui est indépendant de la carte graphique. Les logiciels annexes traitent les coordonnées atomiques des fichiers Protein Data Bank (PDB) dans les descriptions de rendu pour les images composées de rubans, les atomes remplissant l'espace, les liaisons, "ball+stick", etc. Raster3D peut aussi être utilisé pour rendre des images composées dans d'autres logiciels tels que Molscript en 3D avec des surbrillances et des ombrages, etc. La sortie est en fichiers d'images avec 24 bits d'information de couleur par pixel.

Theseus is a program that simultaneously superimposes multiple macromolecular structures. Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. By down-weighting variable regions of the superposition and by correcting for correlations among atoms, the ML superposition method produces very accurate structural alignments.

When macromolecules with different residue sequences are superimposed, other programs and algorithms discard residues that are aligned with gaps. Theseus, however, uses a novel superimposition algorithm that includes all of the data.

This is a program for constructing atomic models of macromolecules from x-ray diffraction data. Coot displays electron density maps and molecular models and allows model manipulations such as idealization, refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers. Validation tools such as Ramachandran and geometry plots are available to the user. This package provides a Coot build with embedded Python support.

Il s’agit d’une bibliothèque pour la cristallographie des macromolécules et la bio-informatique structurale pour travailler avec les fichiers de coordonnées (mmCIF, PDB, mmJSON), les contraintes d’affinement (bibliothèque monomer), les cartes de densité électronique (CCP4) et les données de réflexions cristallographiques (MTZ, SF-mmCIF). Elle comprend les symétries de cristaux, elle sait comment basculer entre les espaces réel et réciproque et elle peut faire quelques autres choses.

Ce paquet fournit l'exécutable principal de gemmi.

CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner. That means: a large number of individual diffraction patterns, each corresponding to a random orientation of the crystal, with little or no rotation or oscillation of the sample. This is exactly the situation encountered when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source, which is the application CrystFEL is primarily designed for. CrystFEL comprises programs for indexing and integrating diffraction patterns, scaling and merging intensities, simulating patterns, calculating figures of merit for the data and visualising the results.

This version has been compiled with opencl support

The Rosetta software suite focuses on the prediction and design of protein structures, protein folding mechanisms, and protein-protein interactions. Rosetta has been consistently successful in CASP and CAPRI competitions. Rosetta also addresses aspects of protein design, docking and structure. The software is the foundation for the Human Proteome Folding Project on the World Community Grid and the Rosetta@home distributed computing project.

The Rosetta software suite is currently licensed for free to users at academic and nonprofit institutions. Over 2000 academic users in more than 32 countries use Rosetta. Commercial entities can use Rosetta by paying a license fee. Revenue from licensing is reinvested in supporting continued software development.

the analysis, rebuilding and visualization of three-dimensional nucleic-acid-containing structures. The software is applicable not only to DNA (as the name 3DNA may imply), but also to complicated RNA structures and DNA-protein complexes. In 3DNA, structural analysis and model rebuilding are two sides of the same coin: the description of structure is rigorous and reversible, thus allowing for its exact reconstruction based on the derived parameters. 3DNA automatically detects all non-cannonical base pairs, base triplets and higher-order associations, and coaxially stacked helices; provides a comprehensive collection of fiber models of regular DNA and RNA helices; generates highly effective schematic presentations that reveal key features of nucleic-acid structures; performs undisturbed base mutations, and have facilities for the analysis of molecular dynamics simulation trajectories.

protein crystallography X-Ray diffraction data. The data may be displayed as a 2-D image, 3-D wire mesh or as integer pixel values. Data may be saved as either tiff or postscript files. Adxv will display data from most current detectors:

• ADSC ccd
• Mar ccd
• Mar image plate (old and new format)
• Raxis II & IV
• Fuji image plate
• Crystallographic Binary Format (CBF)
• XDS .pck files
• European Data Format (EDF)
• NUMPY (NPY)
• Raw binary 8, 16, 32 & 64 bit integer data

reflections, and merges multiple observations into an average intensity: it is a successor program to SCALA

Various scaling models can be used. The scale factor is a function of the primary beam direction, either as a smooth function of Phi (the rotation angle ROT), or expressed as BATCH (image) number (deprecated). In addition, the scale may be a function of the secondary beam direction, acting principally as an absorption correction expanded as spherical harmonics. The secondary beam correction is related to the absorption anisotropy correction described by Blessing (Ref Blessing (1995) ).

The merging algorithm analyses the data for outliers, and gives detailed analyses. It generates a weighted mean of the observations of the same reflection, after rejecting the outliers.

The program does several passes through the data:

• initial estimate of the scales
• first round scale refinement, using strong data using an I/sigma(I) cutoff
• first round of outlier rejection
• if both summation and profile-fitted intensity estimates are present (from Mosflm), then the cross-over point is determined between using profile-fitted for weak data and summation for strong data.
• first analysis pass to refine the "corrections" to the standard deviation estimates
• final round scale refinement, using strong data within limits on the normalised intensity |E|^2
• final analysis pass to refine the "corrections" to the standard deviation estimates
• final outlier rejections
• a final pass to apply scales, analyse agreement & write the output file, usually with merged intensities, but alternatively as file with scaled but unmerged observations, with partials summed and outliers rejected, for each dataset

Anomalous scattering is ignored during the scale determination (I+ & I- observations are treated together), but the merged file always contains I+ & I-, even if the ANOMALOUS OFF command is used. Switching ANOMALOUS ON does affect the statistics and the outlier rejection (qv)

using x-ray crystallographic data. Molecular Replacement(MR) is its core scientific method. BALBES aims to integrate all components, necessary for finding a solution structure by MR, into one system. It consists of a database, scientific programs and a python pipeline. The system is automated so that it needs no user's intervention when running complicated combination of jobs such as model searching, molecular replacement and refinement.

F.Long, A.Vagin, P.Young and G.N.Murshudov "BALBES: a Molecular Replacement Pipeline " Acta Cryst. D64 125-132(2008)

domain structures. Each protein has been chopped into structural domains and assigned into homologous superfamilies (groups of domains that are related by evolution). This classification procedure uses a combination of automated and manual techniques which include computational algorithms, empirical and statistical evidence, literature review and expert analysis.

integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. CCP4 aims to develop and support the development of cutting edge approaches to experimental determination and analysis of protein structure, and integrate these approaches into the suite. CCP4 is a community based resource that supports the widest possible researcher community, embracing academic, not for profit, and for profit research. CCP4 aims to play a key role in the education and training of scientists in experimental structural biology. It encourages the wide dissemination of new ideas, techniques and practice.

interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics, funded by the National Institutes of Health National Center for Research Resources (grant 2P41RR001081) and National Institute of General Medical Sciences (grant 9P41GM103311).

values of the anomalous scattering factors, f' and f'', directly from experimentally measured X-ray fluorescence data. It outputs the f' and f'' spectrum and the appropriate X-ray wavelengths to be used for MAD or SAD experiments.

an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.

structure determination for single or multiple-wavelength anomalous diffraction (SAD/MAD) or single isomorphous replacement (SIRAS) experiments. Crank interfaces with various crystallographic programs and is designed to allow both the automation of the structure determination process, but also allow the user to re-run and optmize results, if necessary.

This version of Crank has interfaces to the programs CRUNCH2 [2] and SHELXD [3] for substructure detection, BP3 [4], [5] for substructure phasing, SOLOMON [6], DM [7], SHELXE [8], PIRATE [9] and RESOLVE [23] for density modification and RESOLVE [24], BUCCANEER [25] and ARP/wARP [10] for automated model building. ARP/wARP uses REFMAC [11] for iterative refinement. Within REFMAC, either the likelihood function restraining phases via Hendrickson-Lattman coefficients [12] or a multivariate likelihood SAD function [13] is used. To calculate FA values needed for substructure detection, crank interfaces with the programs SHELXC [14] or AFRO [15]. For setting up and preparing files, crank using programs from the CCP4 [16] suite, including SFTOOLS [17] and TRUNCATE [18]. Also, crank uses the Kantardjieff-Rupp algorithm [19] which performs a probabilistic Matthew's coefficient [20] calculation for estimating the number of monomers in the asymmetric unit. To visualize the results produced by crank, an interface to COOT [26] is also available.

Crank can be run using its CCP4i [21] interface or via script using the program GCX [22]. Crank's only dependency to produce a density modified map is a licenced CCP4 version 5.99.x or later. If you would like to use the SHELX [13] programs, ARP/wARP [10], RESOLVE [23], [24] and/or BUCCANEER [25] within crank, you must have it installed on your system with the appropriate licence. If these programs do not appear in your path, they will not appear as options in the ccp4i interface.

communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided.

DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers.

DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities.

determination and characterization of dynamical domains in proteins. Its key features are

• computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes
• ease of use: a state-of-the-art graphical user interface
• export of results for visualization and further analysis (VRML, PDB, and MMTK object format)

Dynamical domains are an important concept in the description of protein dynamics. A dynamical domain is a region in a protein which can move essentially like a rigid body relative to other regions. Many, but not all, proteins have dynamical domains, and if they do, the relative movements of the domains are usually related to the function of the protein. The identification of dynamical domains is therefore useful in understanding the function of the protein. However, there are other situations in which the knowledge of dynamical domains is helpful. In structure determination, it can help to predict whether complexation with a ligand, crystal packing, or other external influences can lead to important conformational changes. In protein engineering, it can indicate whether a given modification is likely to change the dynamical behavior of the protein. In experimental observations of protein motion, it can suggest regions of particular interest. In numerical simulations, it can point out the slow motions whose correct sampling must be verified.

DomainFinder is written in Python, a high-level object programming language that is particularly well suited to the demands of scientific computations. The speed-critical parts are implemented in C. For common operations it makes use of the Molecular Modeling Toolkit, a library of Python code for molecular modelling and simulation applications. The results of a domain analysis can be saved with all details in an MMTK data file, which permits all kinds of further analysis.

determination platform is a system which contains several distinct decision-makers which utilize a number of macromolecular crystallographic software programs to produce a software pipeline for automated and efficient crystal structure determination. A large number of possible structure solution paths are encoded in the system and the optimal path is selected by the decision-makers as the structure solution evolves. The processes have been optimised for speed so that the pipeline can be used effectively for validating the X-ray experiment at a synchrotron beamline. Currently, the platform offers SAD, SIRAS, 2W-MAD, 3W-MAD or 4W-MAD phase determination, molecular replacement (MR) and MRSAD phasing. Recently it has been extended to include RIP and MRRIP phasing.

Auto-Rickshaw comes in two flavours : a Beamline Version and an Advanced Version. Both versions use a similar GUI for input, but the Advanced Version requires the sequence information for the protein target in order to build the side chains.

The “Beamline Version” is explicitly designed for use in validation of the X-ray experiment at the synchrotron beamline as soon as the data have been collected and processed. Once the X-ray experiment is validated, the “Advanced Version” can be used for a more complete model building if the resolution of the data permits. The “Advanced Version” of the platform uses ARP/wARP, beta-version of SHELXE, RESOLVE and BUCCANEER

The Auto-Rickshaw platform has been installed on a 64-processors Linux cluster and is remotely accessible to academic users via a web-server . It allows to evaluate the success of their X-ray diffraction experiments in the shortest possible time. This helps to ensure an efficient use of the beam time available. The platform is undergoing continuous development. This includes the improvement of the platform's decision makers, the incorporation of new functionalities as well as continuous software upgrades. An emulation of the Auto-Rickshaw job submission.

Auto-Rickshaw server is freely accessible to users at academic institution upon online registration .

movements in large, multi-chain, biomolecular complexes. The program is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. Unlike the original DynDom (DynDom1D) the method is blind to atomic bonding and atom type and can therefore be applied to biomolecular complexes containing different constituent molecules such as protein, RNA or DNA. At the heart of the method is the use of blocks located at grid points spanning the whole molecule. The rotation vector for the rotation of atoms from each block between the two conformations is calculated. Treating components of these vectors as coordinates means that each block is associated with a point in a “rotation space” and that blocks with atoms that rotate together, perhaps as part of the same rigid domain, will have co-located points. Thus a domain can be identified from the clustering of points from blocks within it. Domain pairs are accepted for analysis of their relative movements in terms of screw axes based upon a set of reasonable criteria. The results provide a depiction of the conformational change within each molecule that is easily understood, giving a perspective that is expected to lead to new insights. It has basically five parameters: a minimum domain size (in number of atoms), a ratio of interdomain displacement to intradomain displacement, a grid length, a block factor, and a block occupancy percentage.

applications especially for online data analysis in the X-ray experiments field. This article describes the features provided by the EDNA framework to ease the development of extensible scientific applications. This framework includes a plugins class hierarchy, configuration and application facilities, a mechanism to generate data classes and a testing framework. These utilities allow rapid development and integration in which robustness and quality play a fundamental role. A first prototype, designed for macromolecular crystallography experiments and tested at several synchrotrons, is presented.

program. Unlike most molecular replacement programs, it does not divide the problem into separate rotation and translation searches. Instead, it uses an evolutionary search algorithm to simultaneously optimize the orientation and position of a search model (1,2). The program operates as follows:

• An initial set of random solutions (random orientations and positions for the search model) is generated.
• The correlation coefficient is alculated for each trial solution.
• A fraction of the highest scoring solutions are retained and used to regenerate a complete set of new trial solutions. This is done by applying random alterations to the orientation angles and translations for each “surviving” solution. The correlation coefficients for the new population are calculated, the population is again regenerated from the top scoring solutions, and this procedure is repeated for a specified number of cycles.

The algorithm provides broad, stochastic, initial sampling of the search space while gradually focusing in on the most promising regions. It allows for efficient searching of the six-dimensional (or higher) space. In general, it is several orders of magnitude faster than a brute-force, systematic, 6-D search. At the end of the evolutionary optimization, a local minimization is performed on the best solution. This is simply a rigid-body refinement of the search molecule.

The program calculates structure factors rapidly by indexing into a molecular transform using the method of Huber and Schneider (3). A traditional structure factor calculation is done only once - for the search model set at the origin of a P1 cell. Subsequent structure factor calculations are done by transforming reflection indices according to the rotations and translations applied to the model and the relationship between the P1 and real cells, interpolating into the grid of P1 structure factors and summing over the symmetry operators of the crystal. This is much faster than an FFT calculation. A simple Babinet-type solvent correction is applied to the calculated structure factors. The values of the solvent correction parameters (k, B) are optimized during the search.

Because of the stochastic nature of the evolutionary optimization process, the correct solution will not be obtained on every run, even with a very good search model. The success rate is dependent on the quality of the model (2). By default, 20 optimization attempts are done, and more may be required if you have a difficult problem. For search models that are poor and at the limit of detection, the search efficiency can be quite low. If you have a molecular replacement problem that has not yielded a solution by any other means, a reasonable last resort is to set up EPMR to do as many runs as your patience and computing resources will allow. As long as the true solution represents the global maximum in the correlation coefficient between Fo and Fc, even if by the slimmest of margins, the algorithm will eventually find it.

EPMR includes the following features:

• the ability to automatically search for multiple copies of a molecule in the asymmetric unit, either sequentially or concurrently
• the ability to search with multiple models, either sequentially or simultaneously (i.e., in competition with each other)
• the ability to use multiple coordinate sets as parts of an “assembly” that comprises the complete search model
• an option to search over all related space groups, either sequentially or simultaneously
• rotation-only and translation-only search modes
• an option to provide static, partial structure
• independent optimization of each segment of a search model during the final rigid-body refinement step
• an option to bypass the evolutionary search and do only local, rigid-body optimization of the model

determination from single-crystal diffraction data. The first version of SHELX was written at the end of the 1960's. The gradual emergence of a relatively portable FORTRAN subset enabled it to be distributed (in compressed form including test data as one box of punched cards) in 1976. SHELX-76 survived unchanged - the extremely compact globally optimized code proved resistant to mutations - until major advances in direct methods theory made an update of the structure solution part necessary (SHELXS-86). Rewriting and validating the least-squares refinement part proved more difficult, but was finally achieved with the release of SHELXL-93. During this time operating systems such as RDOS, VMS and MSDOS, under which FORTRAN and SHELX flourished, rose and fell. Even punched cards became obsolete (except in Florida). The current version SHELX-97 is essentially upwards compatible with SHELX-76, for example the format of the reflection file remained unchanged (Microsoft please note). These programs are used in well over 50% of small-molecule structure determinations. Although SHELX was originally intended only for small molecules, improvements in computing performance and data collection methods have led to increased use of SHELX for macromolecules, especially the location of heavy atoms from MAD, SIR and SAD data using SHELXS (and recently SHELXD and SHELXE), and the refinement of proteins against high-resolution data (2.5A or better) using SHELXL.

SHELX-97 consists of the following programs:

• SHELXS - Structure solution by Patterson and direct methods
• SHELXC - Preparations of files for macromolecular phasing with SHELXD and SHELXE
• SHELXD - Structure solution for difficult problems (and location of heavy atom sites)
• SHELXE - Phases from SHELXD heavy atom sites (and density modification)
• SHELXL - Structure refinement (the version SHELXH is for large structures)
• CIFTAB - Tables for publication via (small molecule) CIF format
• SHELXA - Post-absorption corrections (for emergency use only)
• SHELXPRO - Protein interface to SHELX
• SHELXWAT - Automatic water divining for macromolecules

The program SHELXA was kindly donated by an anonymous user. It applies "absorption corrections" by fitting the observed to the calculated intensities as in the program DIFABS. SHELXA is intended for EMERGENCY USE ONLY, eg. when the world's only crystal falls off before there is time to make proper absorption corrections. Under no circumstances should the results be published; the anonymous author does not wish to be cited in this non-existent publication because it might ruin his reputation!

xdsme is a collection of python scripts made to simplify the processing of crystal diffraction images with the Wolfgang Kabsch's XDS Program (X-ray Detector Software, http://xds.mpimf-heidelberg.mpg.de/). Provided that the diffraction parameters are well recorded in the diffraction image headers, XDS data processing can be started with a simple command line like: