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I have a molecule extracted from the PDB. When I load it into Avogadro, it has some misplaced bond types. I want to correct this, by setting the bond type (single, double) for these bonds. How can I do this?

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  • $\begingroup$ Have a look at this sample PDB file with annotations here. It tells you how you can set single and double/triple/etc. bonds in the file. $\endgroup$ – Philipp Jun 6 '15 at 0:16
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    $\begingroup$ I'd suggest e-mailing the Avogadro mailing lists with such questions. That's the best forum for Avogadro help. :-) $\endgroup$ – Geoff Hutchison Jun 6 '15 at 2:34
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As discussed in the Avogadro website about the draw tool you can change the bond order:

  • By clicking on the bond - the bond order will go from single, to double, to triple, back to single.
  • By setting the bond order and "drawing over" the bond. The new setting (e.g., double) will replace the existing bond.
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  • $\begingroup$ That link is now dead, do you have an up-to-date link to it? Clicking on existing bond does nothing for me. $\endgroup$ – BH2017 Apr 24 '18 at 2:05

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