PAN Blend mx packages

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:

• simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics,
• implicit solvent molecular dynamics of biomolecules ,
• solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design,
• and biomolecular titration studies.

APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms.

This package contains the apbs program and utilities.

AutoDock is a prime representative of the programs addressing the simulation of the docking of fairly small chemical ligands to rather big protein receptors. Earlier versions had all flexibility in the ligands while the protein was kept rather ridgid. This latest version 4 also allows for a flexibility of selected sidechains of surface residues, i.e., takes the rotamers into account.

The AutoDock program performs the docking of the ligand to a set of grids describing the target protein. AutoGrid pre-calculates these grids.

Tento program vykonáva viacnásobné zarovnávanie sekvencií nukleotidov alebo aminokyselín. Rozpoznáva formát vstupných sekvencií a či sú to nukleové kyseliny alebo (DNA/RNA) alebo aminokyseliny (bielkoviny). Môžete si vybrať z viacerých formátov viacnásobného zarovnania ako sú Phylip alebo FASTA. Clustal W je veľmi uznávaný.

Výstup programu Clustal W je možné ručne upravovať pomocou editora zarovnania ako je SeaView alebo jeho sprievodný program Clustal X. Pro zostavovaní modelu z vášho zarovnania je možné ho použiť na vylepšené vyhľadávanie v databáze. Balík Debianu hmmer vytvára takúto formu HMM.

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 je portabilný nástroj na interaktívne kreslenie dát a funkcií riadený z príkazového riadka, podporujúci mnoho výstupných formátov vrátane ovládačov mnohých tlačiarní, (La)TeX, (x)fig, Postscript atď. Výstup do X11 nájdete v balíku gnuplot-x11.

S dátovými súbormi a funkciami je možné pracovať pomocou jazyka podobného jazyku C. Dokáže vyhladzovať, prekladať krivkou, nelineárne prekladanie krivkou a pracovať s komplexnými číslami.

Tento balík slúži na inštaláciu plnohodnotného gnuplot (-qt, -x11 or -nox).

Dokáže zobrazovať, upravovať, analyzovať, spracúvať, ukladať a tlačiť 8- bitové, 16-bitové a 32-bitové obrázky. Číta mnohé obrazové formáty vrátane TIFF, GIF, JPEG, BMP, DICOM, FITS a „raw“. Podporuje „zásobníky“ - série obrázkov, ktoré sa nachádzajú v jednom okne.

Dokáže počítať plochy a štatistiky hodnôt pixlov používateľom vybraných oblastí. Dokáže merať vzdialenosti a uhly. Dokáže tvoriť histogramy hustoty a čiarové profilové kresby. Podporuje štandardné funkcie spracovania obrazu ako zmena kontrastu, zaostrovanie, vyhladzovanie, detekcia hrán a mediánové filtrovanie.

Priestorová kalibrácia poskytuje priestorové miery reálneho sveta ako milimetre. Tiež je dostupná kalibrácia hustoty a škály šedej.

ImageJ vyvíja Wayne Rasband (wayne@codon.nih.gov) na Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules. Jmol might be useful for students, educators, and researchers in chemistry and biochemistry.

File formats read by Jmol include PDB, XYZ, CIF, CML, MDL Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton and 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 is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package includes the following utilities:

• obabel: Convert between various chemical file formats
• obenergy: Calculate the energy for a molecule
• obminimize: Optimize the geometry, minimize the energy for a molecule
• obgrep: Molecular search program using SMARTS pattern
• obgen: Generate 3D coordinates for a molecule
• obprop: Print standard molecular properties
• obfit: Superimpose two molecules based on a pattern
• obrotamer: Generate conformer/rotamer coordinates
• obconformer: Generate low-energy conformers
• obchiral: Print molecular chirality information
• obrotate: Rotate dihedral angle of molecules in batch mode
• obprobe: Create electrostatic probe grid

POV-Ray is a full-featured ray tracer. Ray tracers simulate objects and light sources of the real world to calculate photorealistic, computer generated images. Because of the nature of ray tracing, this process is quite CPU-intensive, at the benefit of more realistic images compared to real time rendering techniques. For example, in POV-Ray, you can model a glass prism, and you will see a spectrum in the resulting image.

POV-Ray by itself is a command-line utility that will take scene descriptions, written in a special easy-to-understand language, to produce ray-traced images (or even a sequence of images, for animations). You can either write those scene-descriptions by hand, or use external tools to generate (parts of) the scene.

povray-includes is highly recommended in addition to this package.

PyMOL je systém na vykresľovanie molekúl cielený na stredné až veľké biomolekuly ako sú bielkoviny. Dokáže tvoriť obrázky a animácie molekúl vo vysokej, produkčnej kvalite.

Medzi jeho vlastnosti patria:

• vizualizácia molekúl, trajektórií molekúl a povrchov kryštalografických dát alebo orbitálov
• zostavovanie a úprava molekúl
• interný raytracing a generátor videoklipov
• úplná rozšíriteľnosť a skriptovateľnosť pomocou rozhrania pre Python

Medzi formátu súborov, s ktorými PyMOL dokáže pracovať patria: PDB, XYZ, CIF, MDL Molfile, ChemDraw, mapy CCP4, mapy XPLOR a mapy Gaussian cube.

Computational Crystallography Toolbox contains following modules:

• annlib_adaptbx:
• boost_adaptbx: wrappers for Boost functionality in CCTBX
• cbflib_adaptbx:
• ccp4io_adaptbx:
• cctbx: Libraries for general crystallographic applications, useful for both small-molecule and macro-molecular crystallography.
• cma_es:
• crys3d: Modules for the display of molecules, electron density, and reciprocal space data.
• dxtbx: The Diffraction Image Toolbox, a library for handling X-ray detector data of arbitrary complexity from a variety of standard formats.
• fable: Fortran EMulation library for porting Fortran77 to C++.
• gltbx: Python bindings for OpenGL
• iotbx: Working with common crystallographic file formats.
• libtbx: The build system common to all other modules. This includes a very thin wrapper around the SCons software construction tool. It also contains many useful frameworks and utilities to simplify application development, including tools for regression testing, parallelization across multiprocessor systems and managed clusters, and a flexible, modular configuration syntax called PHIL (Python Hierarchial Interface Language) used throughout the CCTBX.
• mmtbx: Functionality specific to macromolecular crystallography. This includes all of the machinery required for setup of geometry restraints, bulk solvent correction and scaling, analysis of macromolecular diffraction data, calculation of weighted map coefficients, and most of the methods implemented in phenix.refine. The majority of infrastructure for the MolProbity validation server (and Phenix equivalent) is also located here.
• omptbx: OpenMP interface.
• rstbx: A reciprocal space toolbox to autoindex small molecule Bragg diffraction, given the reciprocal space vectors.
• scitbx: General scientific calculations. his includes a family of high-level C++ array types, a fast Fourier transform library, and a C++ port of the popular L-BFGS quasi-Newton minimizer.
• smtbx: Small-Molecule crystallography.
• spotfinder:
• tbxx:
• wxtbx: wxPython controls used in the Phenix GUI and various utilities

This package provide a selected collection of python modules from the cctbx project.

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 je program na molekulárnu grafiku s účelom vizualizácie proteínov, nukleových kyselín a malých molekúl. Program je určený na zobrazovanie, výuku a tvorbu obrázkov v tlačovej kvalite.

Program načíta súbor so súradnicami molekúl a interaktívne zobrazuje molekulu na obrazovke v rozličných farebných schémach a reprezentáciách molekúl. Medzi momentálne dostupné reprezentácie patria hĺbkové drôtené modely, „Dreidingove“ paličky, gule vypĺňajúce priestor (CPK), gule a paličky, pevné a zreťazené biomolekulárne reťazce, označenia atómov a bodové povrchy.

Medzi podporované vstupné formáty patria Protein Data Bank (PDB), formáty Alchemy od Tripos Associates a Sybyl Mol2, formát (MDL) Mol od Molecular Design Limited, XYZ (XMol) od Minnesota Supercomputer Center (MSC), formát CHARMm, formát CIF a formát mmCIF.

Tento balík nainštaluje dve verzie RasMol, rasmol-gtk s moderným používateľským rozhraním založeným na GTK a rasmol-classic so starým rozhraním Xlib.

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per 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.

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.

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: