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689 results for “crystals”
On the anomalous shapes of native copper crystals from the Michigan Copper Country
<p>Raw NanoSIMS image data files and metadata files with analytical conditions for each analysis. Data associated with manuscript "On the anomalous shapes of native copper crystals from the Michigan Copper Country" by Boulliard, Aléon and Gaillou, accepted in European Journal of Mineralogy, 2021.</p>
Oval rock-crystal intaglio with a flat back, engraved with a one-line brāhmī inscription.
<p>Oval rock-crystal intaglio with a flat back, engraved with a one-line brāhmī inscription. British Museum 1892,1103.136.</p>
Crystal Palace Park Column Piece
A piece of what appears to be a stone stone column in Crystal Palace Park (just north of the central car park), London. Inscription reads: SPECIMEN OF PORTLAND STONE FROM THE ..T.. ..RRIES (?) ..WARD ... (?) WHITEHALL WHARF LONDON 90 photos taken in September 2020 with a Sony a6000 and processed in Reality Capture. Source: Objaverse 1.0 / Sketchfab
Antique Bronze & Crystal Chandelier
Based on an antique 19th century French chandelier, featuring a polished bronze structure, crystal beads and moulding, and 8 candle holders. This model was part of my university project in an introductory 3D modelling course. Since I'm a beginner, there may be some flaws. For example the texture mapping was modified in 3Ds Max, but seems to have lost the UVW map once exported. Any feedback or tips are most welcome! Source: Objaverse 1.0 / Sketchfab
Crystal Palace Statue
A headless statue in Crystal Palace Park just north of the central carpark, London. Could be Dante. Figure is clutching a manuscript. 135 photos taken in September 2020 with a Sony a6000 and processed in Reality Capture. Source: Objaverse 1.0 / Sketchfab
Standing Iguanodon - Crystal Palace Park
The Standing Iguanodon in Crystal Palace Park – Full scan by Stephen Gray and India Carpenter. The model forms part of a survey to assess the structural deterioration of the Standing Iguanodon in Crystal Palace Park. https://en.wikipedia.org/wiki/Crystal_Palace_Dinosaurs The location and dimensions of cracks in the Standing Iguanodon were recorded twice over a three-month period between 2016-2017. The pin drops on the model identify the location of the cracks and include a link to the full dataset, crack report and relevant page numbers. The link also includes the full condition survey data which consists of 4x .obj meshes each with associated texture files, x2 of back right leg and x2 of the entire statue, one with annotations. For a detailed model of the back right leg please see model 'Standing Iguanodon - Back Right Leg'. https://skfb.ly/6pxYX For further information regarding the Crystal Palace Dinosaurs - http://cpdinosaurs.org Source: Objaverse 1.0 / Sketchfab
Crystal Palace Sphinx
One of the six Victorian sphinx statues at Crystal Palace, London. This is the one farthest North. "The sphinxes are based on an original red granite Egyptian sphinx in the Louvre, Paris." (Londonist: https://londonist.com/2016/07/crystal-palace-sphinxes-receive-a-stunning-paint-job) Date: 1850s https://en.wikipedia.org/wiki/The_Crystal_Palace 313 photos taken in February 2020 with a Sony a6000 and processed in Agisoft Metashape. Top of head repainted in Autodesk Mudbox due to missing photos of that area. Source: Objaverse 1.0 / Sketchfab
Simultaneous X-ray diffraction from multiple single crystals of macromolecules
<p>X-ray diffraction datasets from the<br /> publication: K. S. Paithankar, H. O. Sørensen, J. P. Wright, S. Schmidt, H. F. Poulsen and E. F. Garman*</p> <p>Acta Cryst. (2011). D67, 608-618 doi:10.1107/S0907444911015617</p> <p>The potential in macromolecular crystallography for using multiple crystals to collect X-ray diffraction data simultaneously from assemblies of up to seven crystals is explored. The basic features of the algorithms used to extract data and their practical implementation are described. The procedure could be useful both in relation to diffraction data obtained from intergrown crystals and to alleviate the problem of rapid diffraction decay arising from the effects of radiation damage.</p>
Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I
<p>These are X-ray diffraction data from the publication<br> Enderle, M.E, McCarthy, A, Paithankar, K. S, and Grininger, M</p> <p>Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I.</p> <p>Acta Crystallogr F Struct Biol Commun. 2015 Nov;71(Pt 11):1401-7</p> <p>CC-BY-SA license</p> <p>MD5SUMS</p> <p>a774aabcd316b5b200ef5c08b109ba9a crystal-form-II_part-1.tar.lzma</p> <p>3596da75621648cc0ac5ee84b26deab0 crystal-form-II_part-2.tar.lzma</p> <p>8a5410ce3178c814d7a127491e68ca0a crystal-form-I_part-1.tar.lzma</p> <p>259614e1b2cfe089141fb7baa846af7e crystal-form-I_part-2.tar.lzma</p>
X-ray diffraction images for DPF3 tandem PHD fingers co-crystallized with an acetylated histone-derived peptide
<p>This submission includes a tar archive of bzipped diffraction images recorded with the ADSC Q315r detector at the Advanced Photon Source of Argonne National Laboratory, Structural Biology Center beam line 19-ID. Relevant meta data can be found in the headers of those diffraction images.</p> <p>Please find below the content of an input file XDS.INP for the program XDS (Kabsch, 2010), which may be used for data reduction. The "NAME_TEMPLATE_OF_DATA_FRAMES=" item inside XDS.INP may need to be edited to point to the location of the downloaded and untarred images.</p> <p>!!! Paste lines below in to a file named XDS.INP</p> <p>DETECTOR=ADSC MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD= 65000<br /> DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0<br /> DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0<br /> TRUSTED_REGION=0.0 1.05<br /> MAXIMUM_NUMBER_OF_JOBS=10<br /> ORGX= 1582.82 ORGY= 1485.54<br /> DETECTOR_DISTANCE= 150<br /> ROTATION_AXIS= -1.0 0.0 0.0<br /> OSCILLATION_RANGE=1<br /> X-RAY_WAVELENGTH= 1.2821511<br /> INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0<br /> FRACTION_OF_POLARIZATION=0.90<br /> POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0<br /> SPACE_GROUP_NUMBER=20<br /> UNIT_CELL_CONSTANTS= 100.030 121.697 56.554 90.000 90.000 90.000<br /> DATA_RANGE=1 180<br /> BACKGROUND_RANGE=1 6<br /> SPOT_RANGE=1 3<br /> SPOT_RANGE=31 33<br /> MAX_CELL_AXIS_ERROR=0.03<br /> MAX_CELL_ANGLE_ERROR=2.0<br /> TEST_RESOLUTION_RANGE=8.0 3.8<br /> MIN_RFL_Rmeas= 50<br /> MAX_FAC_Rmeas=2.0<br /> VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000<br /> INCLUDE_RESOLUTION_RANGE=50.0 1.7<br /> FRIEDEL'S_LAW= FALSE<br /> STARTING_ANGLE= -100 STARTING_FRAME=1<br /> NAME_TEMPLATE_OF_DATA_FRAMES= ../x247398/t1.0???.img</p> <p>!!! End of XDS.INP</p> <p> </p> <p> </p>
Diffraction images for crystals of the Roseobacter denitrificans nitric oxide reductase (PDB code 4XYD)
<p>X-ray diffraction images corresponding to the dataset from which pdb entry 4XYD was refined.</p> <p>Data was collected at the ESRF.</p> <p>The paper describing the structure is:</p> <p>Structure of the membrane-intrinsic nitric oxide reductase from Roseobacter denitrificans</p> <p>Allister Crow, Yuji Matsuda, Hiroyuki Arata, and Arthur Oubrie</p> <p>doi 10.1021/acs.biochem.6b00332</p> <p> </p>
Example data from a grid scan of a thaumatin crystal recorded at Diamond Light Source beamline I03
<p>Example data recorded at Diamond Light Source beamline I03 as part of ongoing methods development. This is published to allow software authors to benchmark their analysis. Data were recorded with Pilatus3 6M detector as follows:</p> <p># 2016-04-27T10:02:44.731<br /> # Pixel_size 172e-6 m x 172e-6 m<br /> # Silicon sensor, thickness 0.001000 m<br /> # Exposure_time 0.0990000 s<br /> # Exposure_period 0.1000000 s<br /> # Tau = 0 s<br /> # Count_cutoff 1009797 counts<br /> # Threshold_setting: 6350 eV<br /> # Gain_setting: autog (vrf = 1.000)<br /> # N_excluded_pixels = 1161<br /> # Excluded_pixels: badpixel_mask.tif<br /> # Flat_field: FF_p60-0126_E12700_T6350_vrf_m0p100.tif<br /> # Trim_file: p60-0126_E12700_T6350.bin<br /> # Image_path: /ramdisk/2016/cm14451-2/20160427/gw/grid-test/0002/<br /> # Ratecorr_lut_directory: ContinuousStandard_v1.1<br /> # Retrigger_mode: 1<br /> # Wavelength 0.97625 A<br /> # Energy_range (0, 0) eV<br /> # Detector_distance 0.33810 m<br /> # Detector_Voffset 0.00000 m<br /> # Beam_xy (1246.42, 1208.60) pixels<br /> # Flux 0.000000<br /> # Filter_transmission 0.0100<br /> # Start_angle -0.0002 deg.<br /> # Angle_increment 0.0000 deg.<br /> # Detector_2theta 0.0000 deg.<br /> # Polarization 0.990<br /> # Alpha 0.0000 deg.<br /> # Kappa 0.0000 deg.<br /> # Phi 0.0000 deg.<br /> # Phi_increment 0.0000 deg.<br /> # Omega -0.0002 deg.<br /> # Omega_increment 0.0000 deg.<br /> # Chi 0.0000 deg.<br /> # Chi_increment 0.0000 deg.<br /> # Oscillation_axis X.CW<br /> # N_oscillations 1</p> <p> </p>
Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. Part I: Adaptive local approximate models
<p>The global search stage of Crystal Structure Prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II (Habgood, M., Sugden, I. J., Kazantsev, A. V., Adjiman, C. S. & Pantelides, C. C. (2015).<em> J Chem Theory Comput</em> <strong>11</strong>, 1957-1969) program is presented, where the most efficient use of computational effort is ensured via the use of adaptive Local Approximate Model (LAM) placement. The entire search space of relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimise the computational effort expended in high energy regions whilst maximising the accuracy in low energy regions. As the size, complexity, and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule XXVI from the sixth blind test (Reilly <em>et al.</em>, (2016).<em> Acta Cryst. B, accepted</em>.), which is challenging due its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions. </p>
Determination of ti-6242 α and β slip properties using micro-pillar test and computational crystal plasticity
<p>Data for "Determination of ti-6242 α and β slip properties using micro-pillar test and computational crystal plasticity"<br /> http://dx.doi.org/10.1016/j.jmps.2016.06.007</p> <p><br /> Zhen Zhang, Tea-Sung Jun, T. Benjamin Britton and Fionn P.E. Dunne<br /> Department of Materials, Imperial College London, Prince consort Road, London, SW7 2AZ, UK</p> <p>--</p> <p>This experimental data folder contains 3 subfolders:<br /> (1) Micropillar compression videos<br /> (2) Simulation data</p> <p>(3) Data for Figure 4<br /> (4) Data for Figure 6</p> <p>--</p> <p>The simulation data in (2) is ABAQUS input deck containing an example finite element representation of an alpha-beta titanium micropillar subjected to compression loading. This model was calibrated against the experimental data using the first 60s of the stress relaxation period.</p> <p>--</p> <p>If readers need further information, please feel free to contact: zhen.zhang@imperial.ac.uk</p>
Atomic resolution X-ray crystal structure of cisplatin bound to hen egg white lysozyme stored for 5 years ‘on the shelf’
<p>These are the raw diffraction images for crystals 1 and 2 underpinning PDBe code 5LXW.</p>
Single crystal X-ray diffraction data for Hoch_3836 (1-98)
<p>Single crystal X-ray diffraction data for Hoch_3836 (1-987) related to PDBID: 5N5F</p> <p>Data collected at Diamond Light Source, UK.</p>
Single crystal X-ray diffraction data for PFC_05175 (1-99)
<p>Single crystal X-ray diffraction data for PFC_05175 (1-99) related to PDBID: 5N5E</p> <p>Data collected at Diamond Light Source, UK</p>
Supplementary material for the article "The Crystal Cargo Provides a Chronicle of Pre-Caldera Dynamics in Mafic Volcanic Systems: Insights from Colli Albani"
<p>This repository contains the data and supplementary material associated with the manuscript: Ágreda-López M., Musu A., Jorgenson C., Sǎla M., Giordano G., Caricchi L., Stremtan C., Petrelli M. "<strong>The Crystal Cargo Provides a Chronicle of Pre-Caldera Dynamics in Mafic Volcanic Systems: Insights from Colli Albani</strong>".<em> S</em>ubmitted to the Journal<em> Bulletin of Volcanology.</em></p> <div> </div> <p> </p>
SCXRD data PX2-0041_pin01_1 from a DatZ crystal collected on PROXIMA 2A 2023-09-06
<p>Single crystal X-ray diffraction data test data (DatZ) collected on PROXIMA 2A 2023-09-06 during start-up of the check list for Run 4 2023. Puck name = PX2-0041. Pin number = 01. Protein crystal DatZ contains zinc. Data file prefix = PX2-0041_pin01_1.</p>
Supporting Data for: A Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties
<p>Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for relevant systems. These expensive periodic calculations can be circumvented by the usage of embedding methods in which for instance the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. Herein, we extend upon such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We evaluate this approach for the X23 benchmark set of molecular crystals by approximating a periodic hybrid density functional (PBE0+MBD) by embedding multimers into less expensive calculations using a generalized-gradient approximation (GGA) functional (PBE+MBD). We show that trimer interactions are crucial for accurately approximating lattice energies within 1 kJ/mol and might also be needed for further improvement of lattice constants and hence cell volumes. Finally, vibrational properties are already very well captured at the monomer and dimer level, making it possible to approximate vibrational free energies at room temperature within 1 kJ/mol.</p><p>This supporting dataset includes results of PBE0+MBD, PBE+MBD, and multimer embedding calculations for the X23 set of molecular crystals. See the included README.md file for more details. The related preprint can be found at <a href="https://doi.org/10.48550/arXiv.2209.02687">https://doi.org/10.48550/arXiv.2209.02687</a>.</p>
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