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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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