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General discussions (Q&As) / treating abasic site and THF with 3DNA
« on: January 17, 2019, 12:34:02 pm »
Hi Xiao-Jun,
I would like to use 3DNA to get some structural parameters and bending angle of two oligonucleoides: one containing an abasic site in an extrahelical position and without an empty space within the double helix (test_dna_DAP.pdb) , another one containing THF (tetrahydrofuran) in intrahelical position and with the orphan base (test_dna_THF.pdb)
I screened through the forum and I found out that the option --abasic is only applicable for DSSR, can you tell me if the option is also avalaible in 3DNA? If yes, how can I include it in the find_pair and analyze command?
Otherwise, I saw in a post that we can modified manually the find_pair output so that 3DNA can identified these two residues that don't have base atoms. Can you tell me what does the last five columns mean and how can I get these numbers correctly?
Thanks in advance for your help,
Xia
I would like to use 3DNA to get some structural parameters and bending angle of two oligonucleoides: one containing an abasic site in an extrahelical position and without an empty space within the double helix (test_dna_DAP.pdb) , another one containing THF (tetrahydrofuran) in intrahelical position and with the orphan base (test_dna_THF.pdb)
I screened through the forum and I found out that the option --abasic is only applicable for DSSR, can you tell me if the option is also avalaible in 3DNA? If yes, how can I include it in the find_pair and analyze command?
Otherwise, I saw in a post that we can modified manually the find_pair output so that 3DNA can identified these two residues that don't have base atoms. Can you tell me what does the last five columns mean and how can I get these numbers correctly?
Thanks in advance for your help,
Xia