PAN Blend mx packages

APBS è un pacchetto software per la risoluzione numerica delle equazioni di Poisson-Boltzmann (PBE), uno dei modelli continui più popolari per descrivere le interazioni elettrostatiche di soluti molecolari in soluzioni acquose salate. L'elettrostatica del continuo gioca un ruolo importante in molte aree di simulazione biomolecolare, incluse:

• simulazione di processi di diffusione per determinare la cinetica del legame ligando-proteina o proteina-proteina;
• dinamica molecolare del solvente implicito di biomolecole;
• calcolo della solvatazione e dell'energia di legame per determinare le costanti di equilibrio del legame ligando-proteina e proteina-proteina e per facilitare la progettazione razionale di farmaci;
• studi di titolazione biomolecolare.

APBS è stato progettato per valutare in modo efficiente le proprietà elettrostatiche in tali simulazioni per un'ampia gamma di larghezze di scala per permettere lo studio di molecole con decine e fino a milioni di atomi.

Questo pacchetto contiene il programma apbs e le utilità.

AutoDock è un rappresentante di spicco dei programmi che si occupano della simulazione dell'aggancio di ligandi chimici piuttosto piccoli a recettori proteici piuttosto grandi. Le versioni precedenti avevano tutta la flessibilità nei ligandi, mentre la proteina era mantenuta piuttosto rigida. Questa ultima versione 4 permette anche la flessibilità di catene laterali selezionate di residui superficiali, cioè tiene in considerazione i rotameri.

Il programma AutoDock esegue l'aggancio del ligando ad una serie di griglie che descrivono la proteina bersaglio. AutoGrid pre-calcola queste griglie.

Questo programma effettua un allineamento di sequenze multiple di nucleotidi o di amminoacidi. Riconosce il formato di input delle sequenze e se le sequenze sono acidi nucleici (DNA/RNA) o amminoacidi (proteine). Il formato di output può essere selezionato da diversi formati per allineamenti multipli come Phylip o FASTA. Clustal W è molto ben accettato.

L'output di Clustal W può essere modificato manualmente, ma è preferibile farlo con un editor di allineamenti come SeaView o all'interno del suo compagno Clustal X. Quando si costruisce un modello da un allineamento, questo può essere applicato per ricerche migliorate in database. Il pacchetto Debian hmmer crea modelli simili nella forma di un HMM.

Gnuplot è una utilità portabile da riga di comando per tracciare interattivamente grafici a partire da dati e funzioni che supporta differenti formati di uscita, includendo driver per molte stampanti, (La)TeX, (x)fig, PostScript e altri. L'output per X11 è fornito dal pacchetto gnuplot-x11.

I file di dati e le funzioni auto-definite possono essere manipolati attraverso un linguaggio interno simile al C. È in grado di effettuare smussamenti, interpolazioni di spline o interpolazioni non lineari. È in grado di lavorare con numeri complessi.

Questo metapacchetto serve per installare un gnuplot completo di funzionalità (-qt, -x11 o -nox).

Può visualizzare, modificare, analizzare, processare, salvare e stampare immagini a 8, 16 e 32 bit. Può leggere molti formati immagine inclusi TIFF, GIF, JPEG, BMP, DICOM, FITS e "raw". Gestisce "stack": una serie di immagini che condividono un'unica finestra.

Può calcolare statistiche su valori di area e pixel di selezioni definite dall'utente. Può misurare distanze ed angoli. Può creare istogrammi di densità e grafici con linee di contorno. Gestisce le funzioni standard di elaborazione delle immagini come manipolazione del contrasto, sharpening, sfumatura, rilevamento dei bordi e filtri mediani.

La calibrazione spaziale è disponibile per fornire misure dimensionali nel mondo reale in unità quali i millimetri. È anche disponibile la calibrazione della densità o della scala di grigi.

ImageJ è sviluppato da Wayne Rasband (wayne@codon.nih.gov) al Research Services Branch del National Institute of Mental Health di Bethesda nel Maryland, USA.

Jmol è un visualizzatore molecolare in Java per strutture chimiche tridimensionali. Le caratteristiche includono la lettura di una varietà di tipi di file e dell'output di programmi di chimica quantistica, e animazioni di file a più fotogrammi e modalità normali calcolate per programmi quantistici. Comprende funzionalità per prodotti chimici, cristalli, materiali e biomolecole. Jmol potrebbe essere utile a studenti, educatori e ricercatori in chimica e biochimica.

I formati di file letti da Jmol includono PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton e 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 è una cassetta degli attrezzi per la chimica progettata per capire i molti linguaggi dei dati chimici. Permette di cercare, convertire, analizzare o archiviare dati relativi ai campi dei modelli molecolari, chimica, materiali in stato solido, biochimica o aree correlate. Tra le sue funzionalità sono incluse:

• aggiunta e cancellazione di idrogeni;
• supporto per meccanica molecolare;
• supporto per sintassi SMARTS per corrispondenze molecolari;
• rilevamento automatico di caratteristiche (anelli, legami, ibridizzazioni, aromaticità);
• tipizzatore flessibile per atomi e rilevazione di legami multipli dalle coordinate atomiche;
• calcolo della carica parziale con metodo Gasteiger-Marsili.

I formati di file supportati da Open Babel includono PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC e MPQC.

Questo pacchetto include le seguenti utilità:

• obabel: converte tra diversi formati di file relativi alla chimica;
• obenergy: calcola l'energia di una molecola;
• obminimize: ottimizza la geometria, minimizza l'energia di una molecola;
• obgrep: programma di ricerca di molecole che usa modelli SMARTS;
• obgen: genera le coordinate 3D per una molecola;
• obprop: stampa proprietà standard delle molecole;
• obfit: sovrappone due molecole in base ad un modello;
• obrotamer: genera coordinate conformero/rotamero;
• obconformer: genera conformeri a bassa energia;
• obchiral: stampa informazioni sulla chiralità delle molecole;
• obrotate: ruota gli angoli diedri delle molecole in modalità non interattiva;
• obprobe: crea una griglia di sonde elettrostatiche.

POV-Ray è un ray tracer completo. I ray tracer simulano oggetti e sorgenti di luce del mondo reale per calcolare immagini fotorealistiche, generate dal computer. A causa della natura del ray tracing, questo procedimento fa un uso piuttosto intensivo della CPU, a beneficio di immagini più realistiche in confronto alle tecniche di rendering in tempo reale. Per esempio, in POV-Ray, si può modellare un prisma di vetro e si vedrà lo spettro luminoso nell'immagine risultante.

POV-Ray in sé è un'utilità a riga di comando che prende descrizioni di scene, scritte in un linguaggio speciale facile da comprendere, per produrre immagini in ray tracing (o perfino una sequenza di immagini, per animazioni). Si può scrivere tali descrizioni di scene a mano o usare strumenti esterni per generare le scene o loro parti.

povray-includes è fortemente raccomandato in aggiunta a questo pacchetto.

PyMOL è un sistema di grafica per molecole pensato per biomolecole medie o grandi, come proteine. Può generare immagini grafiche e animazioni di molecole di alta qualità pronte per la pubblicazione.

Le funzionalità includono:

• visualizzazione di molecole, traiettorie molecolari e superfici di dati di cristallografia o orbitali;
• costruttore e scultore molecolare;
• raytracer e generatore di filmati interno;
• completamente estensibile e gestibile da script tramite interfaccia Python.

Tra i formati file che PyMOL può leggere sono inclusi PDB, XYZ, CIF, MDL Molfile, ChemDraw, mappe CCP4, mappe XPLOR e mappe gaussiane cubiche.

Python 2, il linguaggio interattivo di alto livello orientato agli oggetti, include una vasta libreria di classi ricca di chicche per la programmazione su reti, amministrazione di sistema, suoni e grafica.

Questo è un pacchetto di dipendenza che dipende dalla versione di Python 2 in Debian (attualmente la 2.7).

RasMol è un programma di disegno molecolare progettato per visualizzare proteine, acidi nucleici e piccole molecole. Il programma è volto a fini illustrativi, didattici e alla produzione di immagini di qualità per la pubblicazione.

Il programma legge da un file le coordinate molecolari e visualizza interattivamente la molecola sullo schermo in una varietà di colori e di rappresentazioni. Attualmente le rappresentazioni disponibili includono insiemi di linee, con segmenti cilindrici rappresentanti i legami, con sfere solide (CPK), con palline e bastoncini, con nastri macromolecolari (sia nastri solidi ombreggiati che filamenti paralleli), con etichette per gli atomi e superfici punteggiate.

I formati di input attualmente supportati comprendono: Protein Data Bank (BPD), i formati Mol2 per Alchemy e Sybyl della Tripos, il formato Mol della Molecular Design Limited (MDL), il formato XMol XYZ del Minnesota Supercomputer Center (MSC), il formato CHARMm, il formato CIF e il formato mmCIF.

Questo pacchetto installa due versioni di RasMol, rasmol-gtk ha una moderna interfaccia basata su GTK e rasmol-classic è la vecchia versione con la GUI Xlib.

Raster3D è un insieme di strumenti per generare immagini raster di alta qualità di proteine o di altre molecole. Il programma principale fa il rendering di superfici di sfere, triangoli, cilindri e quadriche con punti luce riflessi, Phong shading e ombreggiature. Usa un algoritmo Z-buffer software efficiente che è indipendente da ogni hardware grafico. Programmi ausiliari elaborano coordinate atomiche da file PDB in descrizioni di rendering per immagini composte da nastri, atomi che riempono lo spazio, legami, sfere e stecche, ecc. Raster3D può anche essere usato per fare il rendering di immagini composte in altri programmi come Molscript in glorioso 3D con effetto luci, ombreggiatura, ecc. L'output è composto da file di immagini di pixel con 24 bit di informazioni sul colore per pixel.

Theseus è un programma che sovrappone simultaneamente strutture macromolecolari multiple. Trova la soluzione ottimale al problema della sovrapposizione usando il metodo della massima verosimiglianza. Dando meno peso alle regioni variabili della sovrapposizione e apportando correzioni in base alle correlazioni tra gli atomi, il metodo della massima verosimiglianza per la sovrapposizione produce allineamenti strutturali molto accurati.

Quando vengono sovrapposte macromolecole con differenti sequenze di residui, gli altri programmi ed algoritmi non tengono conto dei residui allineati con gap. Theseus, invece, usa un algoritmo di sovrapposizione innovativo che include tutti i dati.

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.

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.

Library for macromolecular crystallography and structural bioinformatics. For working with coordinate files (mmCIF, PDB, mmJSON), refinement restraints (monomer library), electron density maps (CCP4), and crystallographic reflection data (MTZ, SF-mmCIF). It understands crystallographic symmetries, it knows how to switch between the real and reciprocal space and it can do a few other things.

This package contains main gemmi executable.

software. It provides fundamental and advanced methods and algorithms usefull in the scientific fields of crystallography[1], chemistry, physics and biology. It also provides Libraries for general scientific computing. The package is organized as a set of ISO C++ classes with Python bindings.

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: