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CrystalCMP: automatic comparison of molecular structures.

Jan Rohlíček1, Eliška Skořepová1

  • 1Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, Prague 18221, Czech Republic.

Journal of Applied Crystallography
|July 21, 2020
PubMed
Summary

New CrystalCMP software features automated molecular packing comparison. This method identifies identical crystal structures and potential errors in databases like the Cambridge Structural Database (CSD).

Keywords:
comparisonsfragment selectionsmolecular packingsimilarity

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Area of Science:

  • Crystallography
  • Materials Science
  • Computational Chemistry

Background:

  • Accurate comparison of molecular packing is crucial for understanding crystal structures.
  • Existing methods for comparing crystal structures can be labor-intensive and prone to error.
  • The Cambridge Structural Database (CSD) is a vital resource but may contain redundancies or errors.

Purpose of the Study:

  • To introduce an automated procedure for comparing molecular packing within the CrystalCMP software.
  • To enhance the efficiency and accuracy of crystal structure analysis.
  • To identify identical packing arrangements and potential data errors in crystallographic databases.

Main Methods:

  • Development of an automated fragment selection process for molecular comparison.
  • Replacement of traditional angle calculations with root-mean-square deviation (RMSD) of atomic positions for packing comparison.
  • Testing the procedure on a large dataset from the Cambridge Structural Database (CSD).

Main Results:

  • Successful implementation of an automated molecular packing comparison procedure in CrystalCMP.
  • Generation of freely available HTML reports detailing comparison results.
  • Estimation of a reliable threshold for identifying identical molecular packing.
  • Identification of duplicate entries and potentially incorrect space groups within the CSD.

Conclusions:

  • The automated CrystalCMP procedure significantly improves the efficiency of molecular packing comparison.
  • The method provides a robust tool for data validation and quality control in crystallographic databases.
  • This development facilitates more reliable analysis of crystal structures and aids in database curation.