Messages

1

General discussions (Q&As) / Re: Analyzing some pdb files of bent DNA

« on: January 15, 2013, 11:30:57 am »

Thank you Dr.Xiang-Jun. I was wondering how the kinks or breaks are defined in 3DNA. There are 4 such similar bent DNA pdbs: 2O8B, 2O8C, 2O8D and 2O8E. The kinks were seem to be identified in the first 3 and not the last one. Structurally superimposing at the kinked area, no such significant visual differences were observed. So, how the breaks were identified in the first three and not the last. I am missing something here, I think.

2

General discussions (Q&As) / Analyzing some pdb files of bent DNA

« on: January 14, 2013, 03:09:29 pm »

Hello,
I was trying the web 3DNA interface to analyze the bent DNA for pdbid: 2O8B.pdb or 2O8C.pdb. The local base pair step parameters at the site of non canonical base pair are shown as ----. Also Guanine is designated as 'g', not 'G'. Is there some problem with pdb file or something is not recognized by 3DNA?

Thank you in advance
Regards
Monika