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**Avogadro version: (please complete the following information from the About box):**
- Avogadrolibs: 1.98.0-eed1ba848a8bbae6d50205eda16e1046a760e36e
- Qt: 5.15.2 GCC 64-bit
**Desktop version: …
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Hi,
I encountered an issue when using reduce2 to add hydrogens to my protein. Some amino acids have an extra hydrogen atom added to their amide bonds, which caused problems in my subsequent protein …
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Keyboard shortcut and perhaps a very few always outside buttons.
· Passivate all open bonds with hydrogens (now only in the mouse menu I think)
· Start a minimization.
· Sound effects toggle (??)…
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Is there any meaningful filter that can be applied to the top 20 designs to narrow down to the top 10 or 5 candidates? What has been your experience?
1. Perhaps just search for diversity of binder …
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We should add the possibility to include a switching function on the angle to define a hydrogen bond. I do not know if there is a conventional way to do it.
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Hi
I installed pycontact on 2 machines (Mac and Linux) by following the installation instructions in the tutorial and calculated the intra-protein contacts on trajectory. But I am getting H-bond per…
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I encountered a problem when using YASARA to calculate hydrogen bonds, PIPI bonds, ca-pi bonds and saltbrige between proteins and small molecules.
My yasara version is: 22.5.22.
The command I used…
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to implement the workflow for:
- changes in Interaction Strengths (both for stability (intra) and local-interaction (inter)
- decision tree for hub and stability
- changes in the paths of interact…
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The second part of the SHEET lines stores hydrogen bonds to previous beta-strands that indicate strand packing register e.g. 2tbv has the following.
```
SHEET 1 S1A 4 VAL A 103 ASN A 117 0 …