Messages

1

RNA structures (DSSR) / Re: How 3DNA-DSSR define RNA junctions?

« on: January 07, 2015, 11:54:33 am »

Dear Xiangjun,

Thank you for your reply and your information!  Then in my case I can only test several models and analyze the output. I am looking forward to seeing the details in the coming paper.

Thank you so much,
Chen

2

RNA structures (DSSR) / How 3DNA-DSSR define RNA junctions?

« on: January 07, 2015, 12:08:21 am »

Dear developer,

Hello! I am using 3DNA-DSSR to find junctions in RNA structures, but I am just curious about the criteria for the RNA structure elements to be a junction so that appears in the PDB file:

1) The length of each stem
2) Do other structure elements that do not belong to the junction on the secondary structure level but is close to the junction on the tertiary structure level count?

I do appreciate your help!

Thank you so much,
Chen

3

RNA structures (DSSR) / Re: [Q] Can 3DNA output a PDB file of the helix junction(s)?

« 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.

4

RNA structures (DSSR) / [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!