How to validate atom-type assignment using Mogul



August 29, 2023

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  • This video shows you how you can use CCDC’s Mogul Geometry Check to help validate atom type assignments during a crystal structure refinement by comparing bond lengths, angles and torsions against the Mogul library of data. We show how the program can pick up potential errors by running a geometry check on a structure than has deliberately had atoms misassigned by our team for demonstration purposes. The incorrect structure file created for this demonstration can be downloaded here: For the correct structure see or search for refcode “ODECAF” in Mercury or ConQuest. The demonstration includes editing and assigning bond types, running Mogul Geometry Check and analysing results. In this video you will find: -0:05 An introduction to using CCDC’s Mogul as a structure validation tool -01:08 Loading and editing bond-types in a trial structure in CCDC’s Mercury -01:38 Setting up and running Mogul Geometry Check on the trial structure -02:10 Viewing and analysing the results of the geometry check -02:56 Visualizing atomic displacement parameters -03:28 Loading and assessing an alternative model in Mercury -03:50 Running Mogul on the revised model -04:00 Viewing and analysing the results of the geometry check on the revised model -05:00 Conclusions and further resources To learn more about how Mogul works and more details about how to run a Mogul Geometry Check, and how to read and interpret the results, try our free “Analysing molecular geometries 101 – basics of Mogul” CSDU Module here: and see this playlist: Note: this demonstration assumes knowledge of how to use Mercury. You can find guides to using Mercury here in our free self-guided workshops and also in our CSDU module “Visualization 101 – Visualizing structural chemistry data with Mercury” here: You can also find helpful tips on how to view atom labels in Mercury in our video here:

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