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Author Topic: [Q] Can 3DNA output a PDB file of the helix junction(s)?  (Read 4443 times)

Offline hume

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[Q] Can 3DNA output a PDB file of the helix junction(s)?
« on: September 22, 2014, 03:27:37 pm »
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!
« Last Edit: September 22, 2014, 03:31:21 pm by hume »

Offline xiangjun

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Re: [Q] Can 3DNA output a PDB file of the helix junction(s)?
« Reply #1 on: September 23, 2014, 12:47:28 am »
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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline xiangjun

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Re: [Q] Can 3DNA output a PDB file of the helix junction(s)?
« Reply #2 on: September 24, 2014, 02:45:21 pm »
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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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* DSSR 2.0 has superseded the 3DNA v2.4 suite

Offline hume

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Re: [Q] Can 3DNA output a PDB file of the helix junction(s)?
« Reply #3 on: September 24, 2014, 08:48:47 pm »
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.

 

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.