All Possible Base Pairs

[pfeyzi]

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

[xiangjun]

Hi Parivash,

Thanks for your interest in using 3DNA. The find_pair -p command should give you a list of all pairs, canonical or not. Please provide a concrete example to illustrate what base pairs are missing.

As for the availability of x3dna-dssr, please see the post "No more grant funding for 3DNA/DSSR" (http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/). You could use http://skmatics.x3dna.org to analyze/visualize a structure using x3dna-dssr.

Hope this helps.

Xiang-Jun