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Messages - sgu0752

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1
Bug reports / Uncaught exception error
« on: July 21, 2021, 08:54:34 pm »
Hi xiangjun,

I use v1.9.4-2019jul08 of 3DNA-DSSR to analyze PDB structures, and I encountered an error looking at a relatively recent NMR structure 6jwe.

Code: [Select]
x3dna-dssr --more --loop=with-stems --json -i=6jwe.pdb -o=6jwe.json
Processing file ‘6jwe.pdb’
  total number of nucleotides: 20
  total number of base pairs: 18
Uncaught exception ‘Assertion failed’ raised at [fncs_hbond.c:826]
aborting...

Thanks in advance!

2
General discussions (Q&As) / H-bonding information
« on: June 11, 2019, 03:52:55 pm »
Hi,

I'm analyzing the hydrogen bonding interactions of CC mismatches in DNA, and I came across some interesting hydrogen bonding symbols. While I know that the hyphen '-' between two atoms indicates hydrogen bonding, what does '*' represent? Is it because the hydrogen donor/acceptor roles are vague?

I've attached the summary file below of my results.

Thanks for your time.

Stephanie

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.