Search

One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step that could extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). To the extent that different states adopt different molecular structures, one expects to observe differences in the crystals; each of the polystates will create a polymorph of the crystals. After mixed-state diffraction data have been measured, deliberately or inadvertently, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here, this problem is addressed using a simple multi-factor clustering approach that classifies each data set using independent observables, thereby assigning each data set to the correct location in conformational space. This procedure is illustrated using two independent observables, unit-cell parameters and intensities, to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. It is observed that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.

The Follower algorithm was developed to examine the properties of continuous functions and to verify their computer implementations. In particular, we studied measures for distances between unit cells.

These are lecture notes from a one semester course on Data Communications taught at NYU in the 1980's. These notes were written by Dr. Herbert J. Bernstein and the late Professor Max Goldstein and, along with the companion lecture notes on Network Design provide components essential to a more modern book that is under development. Even though, indeed especially because an extensive rewrite and extension is needed for the new work, making these lecture notes accessible is needed to connect the modern work to its past. We will study the tools and techniques needed to deal with communications between computers and the real world and to deal with communications among pieces of computer hardware. We will consider communications systems and media, bandwidth limitations, channel sharing and grouping, data formatting, error detection and correction, protocols, networks, I/O driver design, operating system interfaces and human interfaces.

Here we present two robotic sample changers integrated into the experimental stations for the macromolecular crystallography (MX) beamlines AMX and FMX, and the biological small-angle scattering (bioSAXS) beamline LiX. They enable fully automated unattended data collection and remote access to the beamlines. The system designs incorporate high-throughput, versatility, high-capacity, resource sharing and robustness. All systems are centered around a six-axis industrial robotic arm coupled with a force torque sensor and in-house end effectors (grippers). They have the same software architecture and the facility standard EPICS-based BEAST alarm system. The MX system is compatible with SPINE bases and Unipucks. It comprises a liquid nitrogen dewar holding 384 samples (24 Unipucks) and a stay-cold gripper, and utilizes machine vision software to track the sample during operations and to calculate the final mount position on the goniometer. The bioSAXS system has an in-house engineered sample storage unit that can hold up to 360 samples (20 sample holders) which keeps samples at a user-set temperature (277 K to 300 K). The MX systems were deployed in early 2017 and the bioSAXS system in early 2019.

Methods of generating random unit-cell data for testing software are discussed. Working within the space S 6 appears to be the most expeditious.

KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer `distances' among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences. If the data sets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. When starting from incomplete data sets, one applies KAMO twice, first using unit-cell parameters. In this step, either the simple cell vector distance of the original BLEND or the more sensitive NCDist is used. This step tends to find clusters of sufficient size such that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between reflections with a common hkl to merge clusters in a way that is sensitive to structural differences that may not have perturbed the unit-cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent of one another, it should be possible to greatly improve the efficacy of data-clustering software by using a multi-stage partitioning strategy. Here, one possible approach to multi-stage data clustering is demonstrated. The strategy is to use unit-cell clustering until the merged data are sufficiently complete and then to use intensity-based clustering. Using this strategy, it is demonstrated that it is possible to accurately cluster data sets from crystals that have subtle differences.

The transformations from the primitive cells of the centered Bravais lattices to the corresponding centered cells have conventionally been listed as three-by-three matrices that transform three-space lattice vectors. Using those three-by-three matrices when working in the six-dimensional space of lattices represented as Selling scalars as used in Delone (Delaunay) reduction, one could transform to the three-space representation, apply the three-by-three matrices and then back-transform to the six-space representation, but it is much simpler to have the equivalent six-by-six matrices and apply them directly. The general form of the transformation from the three-space matrix to the corresponding matrix operating on Selling scalars (expressed in space S6 ) is derived, and the particular S6 matrices for the centered Delone types are listed. (Note: in his later publications, Boris Delaunay used the Russian version of his surname, Delone.)

The unit-cell reduction described by Selling and used by Delone (Delaunay) is explained in a simple form., The unit-cell reduction described by Selling and used by Delone (whose early publications were under the spelling Delaunay) is explained in a simple form. The transformations needed to implement the reduction are listed. The simplicity of this reduction contrasts with the complexity of Niggli reduction.

I propose a simple experiment providing evidence that each individual particle is described by a wavefunction of its own. This is contrary to the interpretation of quantum mechanics (QM) apparently favored by Einstein toward the end of his career, at the time his famous autobiographical notes were written. His so-called statistical interpretation holds that individual particles do not have their own wavefunctions; rather, the quantum wavefunction ψ is supposed to ONLY apply to a very multiple, large ensemble of identically prepared particles. For a single particle it fails Einstein criteria of reality and completeness. The experiment proposed here requires heralded single photon counting. In essence we simply prepare many many down-converted signal particles—each heralded by its own accompanying idler that triggers the whole apparatus; prepare the signal photons in different states, assuring that no wavefunction is represented more than once in the entire set of measurement instances. Then take the full set of individual particle counts and show they agree with the implications of standard QM. The exposition makes several connections to Mike Horne’s interests, collaborations and work. The specific property used herein is polarization. For linear polarizations we recover the cosine-squared Law of Malus by preparing individual photons in all possible orientations, then measuring their passage through a fixed orientation analyzer.

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425, 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493, 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015, 1741, 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 1012 photons s−1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 1012 photons s−1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25, 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ, 5, 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5, 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

IUCrJ 7(5), 784 - 792 (2020). doi:10.1107/S2052252520008672, Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules. Over the last few decades, most MX data have been collected at synchrotron beamlines using a large number of different detectors produced by various manufacturers and taking advantage of various protocols and goniometries. These data came in their own formats: sometimes proprietary, sometimes open. The associated metadata rarely reached the degree of completeness required for data management according to Findability, Accessibility, Interoperability and Reusability (FAIR) principles. Efforts to reuse old data by other investigators or even by the original investigators some time later were often frustrated. In the culmination of an effort dating back more than two decades, a large portion of the research community concerned with high data-rate macromolecular crystallography (HDRMX) has now agreed to an updated specification of data and metadata for diffraction images produced at synchrotron light sources and X-ray free-electron lasers (XFELs). This `Gold Standard' will facilitate the processing of data sets independent of the facility at which they were collected and enable data archiving according to FAIR principles, with a particular focus on interoperability and reusability. This agreed standard builds on the NeXus/HDF5 NXmx application definition and the International Union of Crystallography (IUCr) imgCIF/CBF dictionary, and it is compatible with major data-processing programs and pipelines. Just as with the IUCr CBF/imgCIF standard from which it arose and to which it is tied, the NeXus/HDF5 NXmx Gold Standard application definition is intended to be applicable to all detectors used for crystallography, and all hardware and software developers in the field are encouraged to adopt and contribute to the standard., Published by Chester

In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata. In this paper, we discuss three important components of this problem-improved approaches to the clustering of images to better support experiments on polymorphs and dynamics, recent and upcoming changes in metadata for Eiger images, and software to rapidly validate images in the revised Eiger format.

Given a matrix for transforming vectors in the three-space of unit-cell edge vectors, the corresponding matrix to transform vectors in the six-space of Delone scalars is derived., The transformations from the primitive cells of the centered Bravais lattices to the corresponding centered cells have conventionally been listed as three-by-three matrices that transform three-space lattice vectors. Using those three-by-three matrices when working in the six-dimensional space of lattices represented as Selling scalars as used in Delone (Delaunay) reduction, one could transform to the three-space representation, apply the three-by-three matrices and then back-transform to the six-space representation, but it is much simpler to have the equivalent six-by-six matrices and apply them directly. The general form of the transformation from the three-space matrix to the corresponding matrix operating on Selling scalars (expressed in space S6) is derived, and the particular S6matrices for the centered Delone types are listed. (Note: in his later publications, Boris Delaunay used the Russian version of his surname, Delone.)

To build a global quantum communication network, low-transmission, fiber-based communication channels can be supplemented by using a free-space channel between a satellite and a ground station on Earth. We have constructed a system that generates hyperentangled photonic "ququarts" and measures them to execute multiple quantum communication protocols of interest. We have successfully executed and characterized superdense teleportation, a modified remote-state preparation protocol that transfers more quantum information than standard teleportation, for the same classical information cost, and moreover, is in principle deterministic. Our measurements show an average fidelity of $0.94\pm0.02$, with a phase resolution of $\sim7^{\circ}$, allowing reliable transmission of $>10^5$ distinguishable quantum states. Additionally, we have demonstrated the ability to compensate for the Doppler shift, which would otherwise prevent sending time-bin encoded states from a rapidly moving satellite, thus allowing the low-error execution of phase-sensitive protocols during an orbital pass. Finally, we show that the estimated number of received coincidence counts in a realistic implementation is sufficient to enable faithful reconstruction of the received state in a single pass., 34 pages, 14 figures, 3 tables

Algorithms for quantifying the differences between two lattices are used for Bravais lattice determination, database lookup for unit cells to select candidates for molecular replacement, and recently for clustering to group together images from serial crystallography. It is particularly desirable for the differences between lattices to be computed as a perturbation-stable metric, i.e. as distances that satisfy the triangle inequality, so that standard tree-based nearest-neighbor algorithms can be used, and for which small changes in the lattices involved produce small changes in the distances computed. A perturbation-stable metric space related to the reduction algorithm of Selling and to the Bravais lattice determination methods of Delone is described. Two ways of representing the space, as six-dimensional real vectors or equivalently as three-dimensional complex vectors, are presented and applications of these metrics are discussed. (Note: in his later publications, Boris Delaunay used the Russian version of his surname, Delone.)

Quantum mechanics (QM) is the physics of atoms and their constituents. Under reductionism, QM should provide the solid reality for our world, as Einstein insisted. Instead, quantum properties depend strongly on their observer; they are empty (śūnya) until co-dependently created. So physics provides a time-dependent, co-emergent reality (which I designate realitty) reminiscent of śūnyatā.

Many problems in crystallography and other fields can be treated as nearest-neighbor problems. The neartree data structure provides a flexible way to organize and retrieve metric data. In some cases, it can provide near-optimal performance.NearTreeis a software tool that constructs neartrees and provides a number of different query tools.

Version 2.0 of the CIF format incorporates novel features implemented in STAR 2.0. Among these are an expanded character repertoire, new and more flexible forms for quoted data values, and new compound data types. The CIF 2.0 format is compared with both CIF 1.1 and STAR 2.0, and a formal syntax specification is provided.

The Frontier Microfocus Macromolecular Crystallography (FMX) beamline at the National Synchrotron Light Source II with its 1 µm beam size and photon flux of 3 × 1012 photons s−1 at a photon energy of 12.66 keV has reached unprecedented dose rates for a structural biology beamline. The high dose rate presents a great advantage for serial microcrystallography in cutting measurement time from hours to minutes. To provide the instrumentation basis for such measurements at the full flux of the FMX beamline, a high-speed, high-precision goniometer based on a unique XYZ piezo positioner has been designed and constructed. The piezo-based goniometer is able to achieve sub-100 nm raster-scanning precision at over 10 grid-linepairs s−1 frequency for fly scans of a 200 µm-wide raster. The performance of the scanner in both laboratory and serial crystallography measurements up to the maximum frame rate of 750 Hz of the Eiger 16M's 4M region-of-interest mode has been verified in this work. This unprecedented experimental speed significantly reduces serial-crystallography data collection time at synchrotrons, allowing utilization of the full brightness of the emerging synchrotron radiation facilities.

Superdense Teleportation (SDT) is a suitable protocol to choose for an advanced demonstration of quantum communication in space. We have taken further steps towards the realization of SDT in such an endeavor. Our system uses polarization and time-bin hyperentanglement via non-degenerate spontaneous parametric downconversion to implement SDT of 4-dimensional equimodular states. Previously, we have shown high fidelity (>90p) SDT implementation and the feasibility to perform SDT on an orbiting platform by correcting the Doppler shift. Here we discuss new analysis of the received state reconstruction performance in the presence of high channel loss and multiple pair events. Additionally, initial characterization of a waveguide-based entanglement source intended for space will be presented.

ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077.

A description is presented of the NeXus data format for X-ray and neutron scattering and muon spectroscopy., NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitions for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.

Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having “unknown function”. Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed.

KAMO and Blend provide particularly effective tools to manage automatically the merging of large numbers of datasets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending Blend to support additional clustering options such as use of more accurate cell distance metrics and use of reflection-intensity correlation coefficients to infer “distances” among sets of reflec- tions. This increases the sensitivity to differences in unit cell parameters and allows for clustering to assemble nearly complete datasets on the basis of intensity or ampli- tude differences. If datasets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. If starting from incomplete datasets, one applies KAMO twice, first using cell parameters. In this step we use either the simple cell vector distance of the original Blend, or we use the more sensi- tive NCDist. This step tends to find clusters of sufficient size so that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between the reflections having a common hkl to merge clusters in a way sensitive to structural differences that may not have perturbed the cell parameters sufficiently to make meaningful clusters.Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into cate- gories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent from one another, it should be possible to greatly improve the efficacy of data clustering software by using a multi-stage partitioning strategy. Here, we have demonstrated one possible approach to multi-stage data clustering. Our strategy is to use unit-cell clustering until merged data is sufficiently complete then to use intensity-based clustering. We have demonstrated that, using this strategy, we are able to accurately cluster datasets from crystals that have subtle differences.

Niggli reduction can be viewed as a series of operations in a six-dimensional space derived from the metric tensor. An implicit embedding of the space of Niggli-reduced cells in a higher-dimensional space to facilitate calculation of distances between cells is described. This distance metric is used to create a program,BGAOL, for Bravais lattice determination. Results fromBGAOLare compared with results from other metric based Bravais lattice determination algorithms. This embedding depends on understanding the boundary polytopes of the Niggli-reduced coneNin the six-dimensional spaceG6. This article describes an investigation of the boundary polytopes of the Niggli-reduced coneNin the six-dimensional spaceG6by algebraic analysis and organized random probing of regions near one-, two-, three-, four-, five-, six-, seven- and eightfold boundary polytope intersections. The discussion of valid boundary polytopes is limited to those avoiding the mathematically interesting but crystallographically impossible cases of zero-length cell edges. Combinations of boundary polytopes without a valid intersection in the closure of the Niggli cone or with an intersection that would force a cell edge to zero or without neighboring probe points are eliminated. In all, 216 boundary polytopes are found. There are 15 five-dimensional boundary polytopes of the fullG6Niggli coneN.

A database of lattices using theG6representation of the Niggli-reduced cell as the search key provides a more robust and complete search than older techniques. Searching is implemented by finding the distance from the probe cell to other cells using a topological embedding of the Niggli reduction inG6, so that all cells representing similar lattices will be found. The embedding provides the first fully linear measure of distances between unit cells. Comparison of results with those from older cell-based search algorithms suggests significant value in the new approach.

Macromolecular Crystallography (MX) is becoming a big data science straining the capabilities of computers and networks. New techniques of serial crystallography are allowing new science to be done but they are increasing the heterogeneity of the data that must be handled. Two new beamlines at the National Synchrotron Light Source-II, for Frontier Macromolecular Crystallography (FMX) and for highly Automated Macromolecular Crystallography (AMX), are beginning user operation in 2016, and are dealing with these big data issues. This work is contributing to a worldwide High Data-Rate Macromolecular Crystallography (HDRMX) collaboration among crystallographic software developers, beamline scientists and controls people to resolve these issues as new high-brightness beamlines and new fast X-ray detectors come into increasing use.