Messages

1

General discussions (Q&As) / Re: All Possible Base Pairs

« on: July 30, 2024, 03:59:27 pm »

Thanks

2

General discussions (Q&As) / Re: All Possible Base Pairs

« on: July 29, 2024, 02:22:23 pm »

Dear Dr. Lu,

Can we find list of tertiary stacks from pdb by using x3DNA? like Example_stacks.dat for RNA.pdb file that I attached.

As I run this command
```
find_pair RNA.pdb bpfile.out
analyze bpfile.out 
```
it generate bunch of files like hstacking.pdb
but I don't know how to get that tertiary stacks list!

3

General discussions (Q&As) / All Possible Base Pairs

« on: June 09, 2024, 07:11:36 pm »

Dear Dr. Lu,
I hope this message finds you well.
I am currently using x3DNA to identify base pairs in my PDB files. I have been using the command
"find_pair -p X.pdb stdout | analyze stdin"
which provides me with the strongest base pairs for each residue. However, I am interested in identifying all possible base pairs, including both canonical and non-canonical pairs, regardless of their strength.
Is there a way to modify the command or use a different tool within x3DNA to obtain a comprehensive list of all possible base pairs for each residue? or can we change its constraints to include all pairs?
Additionally, I found in the new version of x3DNA, x3dna-dssr tool is not available. Is it possible to download the versions which includes that?
Thanks you so much,
Parivash