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CrystalMaker Advice Centre Can I get CrystalMaker to automatically find H-bonds? |
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As with all structures, you can use the Edit > Bonding
window to request that bonds be automatically generated.
An interesting case arises where a structure contains different kinds of bonding between the same element pairs. An example might be a structure with both covalent H--O and hydrogen-bonded H...O bonds. CrystalMaker can separate-out these two bond types - using the fact that they have different bond lengths. The Edit > Bonding window permits multiple bond definitions for the same element pairs, so one could define separate bond specifications to cover, on the one hand, the H--O bonds, and on the other hand, the H...O bonds. One would specify bond ranges of (say) 0 to 1.1 A for the covalent (H--O) bonds and (approximately) 1.2 to 1.8 A for the hydrogen bonds (which are typically around 1.6 A in length). |
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