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General discussions (Q&As) / generating 10.5 bp/turn B-DNA
« on: November 10, 2013, 03:55:16 pm »
Dear Xiang
{Sorry, I posted personal mail earlier. Now I am using "New Topic", hope it goes to all}
I explored your online tools and found them very useful. For Fibre BDNA generic form we can get 36 degree twist and 3.37 rise as default values. I have B-DNA sequence pdb (MY.pdb; also your tool can help to generate directly 10 bp B-DNA) with 10 bp/turn and want same B-DNA sequence as 10.5 bp/turn. Please let me know if following process would be correct to generate 10.5 bp B-DNA:
1) Analyse this MY.pdb (having 10bp/turn) using Analysis tool online.
2) Save the Nucleic Acid Local Base Step Parameters and Local Base-pair Parameters and write on text file. Edit the text file and modify each twist to 34.29 keep rise same as 3.54 (which is obtained as: twist= 360/10.5; and rise = 3.37+ (3.37/2)/10 = 3.5385 ). I am not sure about the rise especially and others. Should I keep other params same?
3) Generate new B-DNA with using this edited parameter file (Reconstruction--> customised model)
Please let me know if this procedure is correct?
kind regards
Jiomm
{Sorry, I posted personal mail earlier. Now I am using "New Topic", hope it goes to all}
I explored your online tools and found them very useful. For Fibre BDNA generic form we can get 36 degree twist and 3.37 rise as default values. I have B-DNA sequence pdb (MY.pdb; also your tool can help to generate directly 10 bp B-DNA) with 10 bp/turn and want same B-DNA sequence as 10.5 bp/turn. Please let me know if following process would be correct to generate 10.5 bp B-DNA:
1) Analyse this MY.pdb (having 10bp/turn) using Analysis tool online.
2) Save the Nucleic Acid Local Base Step Parameters and Local Base-pair Parameters and write on text file. Edit the text file and modify each twist to 34.29 keep rise same as 3.54 (which is obtained as: twist= 360/10.5; and rise = 3.37+ (3.37/2)/10 = 3.5385 ). I am not sure about the rise especially and others. Should I keep other params same?
3) Generate new B-DNA with using this edited parameter file (Reconstruction--> customised model)
Please let me know if this procedure is correct?
kind regards
Jiomm