[Q] Can 3DNA output a PDB file of the helix junction(s)?

[hume]

Hi all,

I am thinking of doing some analysis on RNA junctions of a bunch of PDB files. I am just wondering whether 3DNA can extract the junctions in PDB and output it as a PDB file, as is done for the hairpins/K-turns/etc.

Thank you so much!

[xiangjun]

It is certainly possible for DSSR to output a MODEL/ENDMDL delineated PDB ensemble file for junctions, just as it does for the hairpin loops. I did think about this issue, but then decided to leave it off -- there are already quite a few auxiliary files from DSSR, and I do not want DSSR to look overwhelming.

Since you asked for such functionality, I will consider to add it in the next releases of DSSR. In the meantime, it should be straightforward to extract what you need based on the relevant DSSR output.

Xiang-Jun

[xiangjun]

I've just released DSSR v1.1.7-2014sep24 that outputs three additional auxiliary files (where available): dssr-bulges.pdb, dssr-iloops.pdb and dssr-junctions.pdb in an MODEL/ENDMDL-delineated ensemble format, same as for dssr-hairpins.pdb. Hope this version fits your needs.

Xiang-Jun

[hume]

Thank you so much! I really appreciate it! I am not a programmer and this new feature is really helpful for me to analyze a large amount of PDB files.