PAN Blend mx packages

APBS er et en programpakke til numerisk problemløsning af Poisson- Boltzmann-ligningen, én af de mest populære kontinuum-modeller til beskrivelse af elektrostatisk interaktion mellem molekylære opløsninger i salte, vandholdige medier. Elektrostatisk kontinuum spiller en vigtig rolle i forskellige områder inden for biomolekylær simulering, inklusive:

• simulering af diffusionsprocesser til fastlæggelse af kinetiske ligang-protein- og protein-protein-bindinger,
• implicit opløsning af biomolekyler i molekylær dynamik,
• energiberegninger i hydrater og bindinger til fastlæggelse af ligevægt mellem ligand-protein- og protein-protein-bindingskonstanter, og til at fremme rationelt design af medicin,
• og studier i biomolekylær titrering.

APBS blev designet for effektiv evaluering af elektrostatiske egenskaber for sådanne simuleringer inden for bred række af længdeskalaer for at muliggøre undersøgelsen af molekyler med bestående af ti til millionvise af atomer.

Denne pakke indeholder programmet apbs og redskaber.

AutoDock er en iøjnefaldende repræsentation for programmer der adresserer simuleringen af dokningen af ret små kemiske ligander til ret så store proteinreceptorer. Tidligere versioner havde hele fleksibiliteten i liganderne mens proteinet blev holdt ret så rigidt. Denne seneste version 4 tillader også fleksibilitet for valgte sidekæder for overfladeefterladenskaber, dvs., tage rotamerne i betragtning.

Programmet AutoDock udfører dokning af liganden til et gittersæt der beskriver målproteinet. AutoGrid forhåndsberegner disse gitre.

Dette program udfører en sammenligning af flere nukleotid- eller aminosyresekvenser. Det genkender formatet for inddatasekvenser, og om sekvenser er nukleinsyre (DNA / RNA) eller aminosyre (proteiner). Uddataformatet kan vælges i forskellige formater for flere sammenligninger såsom Phylip eller FASTA. Clustal W er velaccepteret.

Produktionen af ​​Clustal W kan redigeres manuelt, men helst med et justeringssredigeringsprogram som SeaView eller indenfor dens følgesvend Clustal X. Når man bygger en model fra din sammenligning, kan denne anvendes til forbedrede databasesøgninger. Debianpakken HMMER skaber en sådan i form af en HMM.

DIALS-programmet er udviklet helt frit i et samarbejdende miljø. Udviklingsholdene er baseret på Diamond Light Source og CCP4, i UK og på Lawrence Berkeley National Laboratory, USA. I ånden for åben kildekodeudvikling, så er alle velkomne, der ønsker at bidrage til projektet.

For at undgå »genopfindelse af hjulet« så bygger DIALS-projektet på viden indsamlet over mange årtier i feltet indenfor krystallografisk databehandling.

DIALS er skrevet via Python og C++ og gør stærk brug af cctbx for grundlæggende krystallografiske beregninger og meget infrastruktur inklusive et fuldstændigt byggesystem.

Gnuplot er et portabelt kommandolinjedrevet, interaktivt data- og funktions-plotningsredskab, der understøtter en masse uddata-formater, heriblandt drivere til mange printere, (La)TeX, (x)fig og PostScript, og så videre. X11-uddata er blevet pakket i gnuplot-x11.

Datafiler og selvdefinerede funktioner kan manipuleres med et internt, C-lignende sprog. Du kan udføre udjævning, kurvetilpasning eller ikke-lineære fits (Flexible Image Transport System), samt arbejde med komplekse tal.

Denne pakke er til at installere en gnuplot med alle funktioner (-qt, x11 eller -nox).

Det kan vise, redigere, analysere, behandle, gemme og udskrive 8-bit, 16- bit og 32-bit billeder. Det kan læse mange billedformater inklusive TIFF, GIF, JPEG, BMP, DICOM, FITS og »raw«. Det understøtter »stakke«, en serie af billeder som deler et enkelt vinude.

Den kan udarbejde værdistatistikker for områder og billedepunkter fra brugerdefinerede markeringer. Det kan måle afstande og vinkler. Det kan oprette histogrammer over tæthed og plotte linjeprofiler. Det understøtter standardfunktioner til billedbehandling såsom manipulation af kontrast, øget skarphed, udjævning, kantdetektering og median-filtrering.

Rumlig kalibrering er tilgængelig for at tilbyde målinger af dimensioner fra den virkelige verden i enheder som milimeter. Tætheds- eller gråskala- kalibrering er også tilgængelig.

ImageJ er udviklet af Wayne Rasband (wayne@codon.nih.gov), der er ved: the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

Jmol er en Javamolekylær fremviser for tredimensionelle kemiske strukturer. Funktioner inkluderer læsning af en række filtyper og resultater fra quantum-kemiprogrammer og animation af filer med flere rammer samt beregnede normale tilstande fra quantum-programmer. Fremviseren inkluderer funktioner for kemikalier, krystaller, materialer og biomolekyler. Jmol kan være nyttigt for studenter, undervisere og forskere indenfor kemi og biokemi.

Filformater som kan læses af Jmol inkluderer PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton og 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 er en kemisk værktøjskasse, som er designet til at tale mange kemiske data-sprog. Den tillader søgning, konvertering, analyse eller lagring af data fra molekylær modellering, kemi, faste materialer, biokemi eller beslægtede områder. Egenskaber inkluderer:

• Indsættelse og fjernelse af hydrogen
• Understøttelse af molekylær-mekanik
• Understøttelse af SMARTS molekylære syntaks-sammenligninger
• Automatisk registrering af egenskaber (ringe, bånd, hybridisering, aromaticitet)
• Fleksibel bestemmelse af atomtyper og registrering af atomare koordinater med flere bånd
• Gasteiger-Marsili-beregning af delvis ladning

Filformater som Open Babel understøtter inkluderer PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC og MPQC.

Denne pakke inkluderer følgende redskaber:

• obabel: Konverter mellem forskellige kemiske filformater
• obenergy: Beregn energien for et molekyle
• obminimize: Optimer geometrien, minimer energien for et molekyle
• obgrep: Molekylært søgeprogram som anvender mønstre fra SMARTS
• obgen: Opret 3D-koordinater for et molekyle
• obprop: Udskriv standardegenskaber for molekyler
• obfit: Læg to molekyler oveni hinanden baseret på et mønster
• obrotamer: Opret konformer/rotamer-koordinater
• obconformer: Opret konformere med lavt energiniveau
• obchiral: Udskriv informationer om molekylær kiralitet
• obrotate: Roter torsionsvinkel for molekyler i stakkevis tilstand
• obprobe: Opret elektrostatisk sondegitter

POV-Ray er en »lyssporer« med alle funktioner. Lyssporer simulerer objekter og lyskilder fra den virkelige verden til at beregne fotorealistiske, computeroprettede billeder. På grund af lys' natur er denne proces meget cpu-intensiv, men giver mere realistiske billeder sammenlignet med optegningsteknikker i realtid. For eksempel, i POV-Ray, kan du modellere en glasprisme og du vil se et spektrum i billedet.

POV-Ray er i sig selv et redskab for kommandolinjen, som anvender scenebeskrivelser, skrevet i et specielt men nemt at forstå sprog, til at fremstille lyspåvirkede billeder (eller endda en sekvens af billeder, for animationer). Du kan enten skrive disse scenebeskrivelser manuelt, eller bruge ekstern værktøjer til at oprette (dele af) scenen.

Povray-includes anbefales udover denne pakke.

PyMOL er et system til molekylærgrafik målrettet mellemstore til store biomolekyler som proteiner. Det kan fremstille udgivelsesklare billeder og animationer af molekylærgrafik i høj kvalitet.

Egenskaber inkluderer:

• Visualisering af molekyler, molekylærbaner og overflader af data fra krystallografi eller orbitaler
• Molekylærbygger og -skulptør
• Intern strålesporing og filmgenerator
• Fuldt udvidelig og skriptbar via en Python-grænseflade

Filformater som PyMOL kan læse inkluderer PDB, XYZ, CIF, »MDL Molfile«, ChemDraw, CCP4-kort, XPLOR-kort og »Gaussian cube«-kort.

Computational Crystallography Toolbox indeholder de følgende moduler:

• annlib_adaptbx:
• boost_adaptbx: omslag for Boost-funktionalitet i CCTBX
• cbflib_adaptbx:
• ccp4io_adaptbx:
• cctbx: Biblioteker for generel krystallografiske programmer, nyttig for både lille-molekylde og makro-molekyle krystallografi.
• cma_es:
• crys3d: Moduler for visningen af molekyler, elektrontæthed og reciprokke rumdata.
• dxtbx: The Diffraction Image Toolbox, et bibliotek til at håndtere røntgendetektordata med arbitrær kompleksitet fra en række standardformater.
• fable: Fortran EMulation-bibliotek for omkodning af Fortran77 til C++.
• gltbx: Pythonbindinger for OpenGL
• iotbx: Arbejde med fælles krystallografiske filformater.
• libtbx: Byggesystemet fælles for alle andre moduler.
• mmtbx: Funktionalitet specifik for makromolekylære krystallografi.
• omptbx: OpenMP-grænseflade.
• rstbx: En reciprok rumværktøjskasse til automatisk indeksering af små molekyle Bragg-diffraktion, given de reciprokke rumvektorer.
• scitbx: Generelle videnskabelige beregninger. Dette inkluderer en familie af C++-tabeltyper på højt niveau, et hurtigt Fourier-transformationsbibliotek og en C++-omkodning af det populære L-BFGS kvasi-Newton minimeringsprogram.
• smtbx: Lille-molekyle krystallografi.
• spotfinder:
• tbxx:
• wxtbx: wxPython-styring brugt i den grafiske brugerflade Phenix og diverse redskaber

Denne pakke tilbyder en udvalgt samling af Pythonmoduler fra projektet 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.

Simpel Pythonpakke. Den bruges til at tilbyde adgang til datafiler brugt i regressionstest, men indeholder ikke selv nogle af disse data.

Selvom forudsat til brug i et cctbx/DIALS-miljø for test i DIALS, dxtbx, xia2 og relaterede pakker, så har pakken ingen afhængigheder i hverken cctbx eller DIALS, faktisk er alle afhængigheder eksplicit erklæret i filen setup.py og kan installeres via setuptools/pip-metoder. Dette betyder at dials_data nemt kan bruges i andre projekter med adgang til de samme data, og kan bruges i midlertidige miljøer såsom Travis-containere.

Python 3-værktøjer til at læse europæiske XFEL's HDF5-filer.

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 er et molekylært grafikprogram lavet til visualisering af proteiner, xxx syrer og små molekyler. Programmet har som formål at vise, lære og oprette billeder i udgivelseskvalitet.

Programmet læser i en molekylær koordinatfil og viser interaktivt molekylet på skærmen i forskellige farveskemaer og molekylerepræsentationer. Blandt de tilgængelige repræsentationer findes trådgitter med dybdeeffekt, Dreiding-pinde, kalotmodeller (CPK), kugler og pinde, biomolekylære bånd (eller »ribbons«; massive og som tråde), atometiketter samt prikoverflader.

Understøttede filformater inkluderer Protein Data Bank (PDB), Tripos Asscociates' Alchemy- og Sybyl Mo12-formater, Molecular Design Limiteds (MDL) Mol-filformat, Minnesota Supercomputer Centers (MSC) XYZ-format (XMol), CHARMm-format, CIF-format og mmCIF-formatfiler.

Denne pakke installerer to versioner af RasMol: rasmol-gtk har en moderne GTK-baseret brugerflade og rasmol-classic har versionen med den gamle Xlib-grafiske brugerflade.

Raster3D er et sæt af værktøjer for oprettelse af højkvalitets rasterbilleder for proteiner eller andre molekyler. Basisprogrammet optegner sfærer, triangler, cylindere og keglesnitsflader med spejlende fremhævelse, Phong-skygge og skyggelægning. Programmet bruger en effektiv programalgoritme Z-buffer, som er uafhængig af eventuelt udstyr. Yderligere programmer behandler atomare koordinater fra PDB-filer til optegningsbeskrivelser for billeder komponeret for bånd, pladsfyldende atomer, grænser, bold+stav etc. Raster3D kan også bruges til at optegne billeder fremstillet i andre programmer såsom Molscript i strålende 3D med fremhævelser, skyggelægning etc. Resultatet gemmes i billedpunktsfiler med 24-bit farveinformation per billedpunkt.

Theseus er et program, som simultant overlejrer flere makromolekylære strukturer. Theseus finder den optimale løsning til superpositionsproblemet med brug af metoden for maksimal sandsynlighed. Ved at nedvægte variable regioner af superpositionen og ved at rette for korrelationer mellem atomer, fremstiller ML-superpositionsmetoden meget præcise strukturelle sammenligninger.

Når makromolekyler med forskellige sekvenser bliver overlejret, fjerner andre programmer og algoritmer rester som er sammenlignet med huller. Theseus, derimod, bruger en ny superimpositionsalgoritme som inkluderer alle data.

Dette er et program for konstruktion af atomare modeller for makromolekyler fra røntgendiffraktionsdata. Coot viser elektrontæthedskort og molekylære modeller og tillader modelmanipulationer såsom idealisering, forfinelse, manuel rotation/oversættelse, fast-krop tilpasning, ligand-søgning, solvation, mutationer, rotamerer. Valideringsværktøjer som f.eks. Ramachandran og geometriplot er tilgængelige for brugeren. Denne pakke tilbyder en Coot-bygning med indlejret understøttelse af Python.

Bibliotek for makromolekylær krystallografi og strukturel bioinformatik. For arbejdet med koordinatfiler (mmCIF, PDB, mmJSoN), forfinede begrænsninger (monomerbibliotek), elektrontæthedskort (CCP4) og krystallografisk refleksionsdata (MTZ, SF-mmCIF). Biblioteket forstår krystallografiske symmetrier, det ved, hvordan man skifter mellem det virkelige og det gensidige rum, og det kan udføre nogle få andre ting.

Denne pakke indeholder den kørbare fil for 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: