hydrogen bonds #720
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Hi, I'm new to Molecular Nodes and I want to visualize hydrogen bonds in quite simple structure. Is there a way to provide set of atoms indexes (or any similar way) between which I want to create hydrogen bonds visualized as, for example, dotted line? I was trying to do Select Elements by Atomic Number > Select Elements > Topology Find Bonds > Style Sticks > Join Geometry but I cannot make these sticks being dotted sticks and also when I select both hydrogens and oxygens bonds are also created between the same atom type (H–H and O–O). Any help will be much appreciated!
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There isn't currently any good support for hydrogen bond visualisation in MN unfortunately. It's something that is mostly limited by the ability to compute new bonds inside of GN (although these limitations will be addressed in future versions as lists and other data types become available). As for the idea of manually specifying atom indices or something similar, that might be able to be something that is supported in the future. Short answer is that HBond-related visualisation is certainly limited at the moment, mostly due to GN limitations. |
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Okay, thanks a lot for quick reply! |
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There isn't currently any good support for hydrogen bond visualisation in MN unfortunately. It's something that is mostly limited by the ability to compute new bonds inside of GN (although these limitations will be addressed in future versions as lists and other data types become available).
As for the idea of manually specifying atom indices or something similar, that might be able to be something that is supported in the future.
Short answer is that HBond-related visualisation is certainly limited at the moment, mostly due to GN limitations.