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Design Example: Strain Gauge Bridge or Wheatstone Bridge01:15

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The utilization of strain gauges as transducers for converting mechanical strain into electrical signals is a common practice in various engineering applications. These strain gauges are frequently integrated into Wheatstone bridge circuits to accurately measure parameters such as force or pressure. Within this context, each element within the circuit exhibits a resistance that undergoes subtle variations when subjected to mechanical strain. The primary objective is to convert minuscule...
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An ohmmeter is a resistance-measuring device. It works by applying a voltage to a resistor of unknown resistance and measuring the current across the resistor. The resistance value is deduced using Ohm's law. Usually, the standard configuration of an ohmmeter comprises a voltmeter or an ammeter. However, such configurations are limited in accuracy because the meters alter the voltage applied to the resistor and the current that flows through it.
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Multicellular organisms employ a variety of ways for cells to communicate with each other. Gap junctions are specialized proteins that form pores between neighboring cells in animals, connecting the cytoplasm between the two, and allowing for the exchange of molecules and ions. They are found in a wide range of invertebrate and vertebrate species, mediate numerous functions including cell differentiation and development, and are associated with numerous human diseases, including cardiac and...
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Non-merohedral twinning: from minerals to proteins.

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PDB2INS: bridging the gap between small-molecule and macromolecular refinement.

Anna V Lübben1, George M Sheldrick1

  • 1Abteilung für Strukturchemie, Universität Göttingen, Tammannstrase 4, Göttingen, D-37077, Germany.

Journal of Applied Crystallography
|June 26, 2019
PubMed
Summary
This summary is machine-generated.

PDB2INS is a Python program that automates the creation of input files for SHELXL structure refinement. This tool successfully processed 96% of tested Protein Data Bank structures, streamlining crystallographic refinement.

Keywords:
PDB formatSHELXLcrystal structure refinementmacromolecules

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Area of Science:

  • Crystallography
  • Structural Biology
  • Computational Chemistry

Background:

  • Macromolecular structure determination relies on accurate refinement of atomic coordinates.
  • The process of preparing input files for refinement software like SHELXL can be time-consuming and prone to errors.
  • Automating the generation of refinement files can significantly improve efficiency in structural biology workflows.

Purpose of the Study:

  • To introduce PDB2INS, an open-source Python program designed to automate the preparation of .ins and .hkl files for SHELXL refinement.
  • To enable PDB2INS to retrieve necessary data directly from the Protein Data Bank (PDB) archive or PDB_REDO server using a PDB code.
  • To assess the performance and success rate of PDB2INS in generating refinement-ready files for a large dataset of X-ray structures.

Main Methods:

  • PDB2INS utilizes PDB codes to access atomic coordinates from PDB-format files and reflection data from mmCIF or PDB_REDO.
  • The program automatically generates SHELX-format .ins and .hkl files, including necessary restraints.
  • A dataset of 23,5974 X-ray structures from the PDB (2008-2018) with high-resolution data was used for testing.

Main Results:

  • PDB2INS successfully generated input files for SHELXL without user intervention for 96% of the tested structures.
  • The program automatically incorporated appropriate restraints and other necessary parameters for refinement.
  • Subsequent refinement using SHELXL completed successfully for the majority of structures processed by PDB2INS.

Conclusions:

  • PDB2INS is an effective tool for automating the preparation of crystallographic refinement files.
  • The program enhances the efficiency and reduces potential errors in the structure refinement process.
  • PDB2INS facilitates the use of SHELXL for a wide range of X-ray crystallographic datasets.