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Messages - jyesselm

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RNA structures (DSSR) / Re: DSSR issue --json and --analyze
« on: April 20, 2020, 12:45:31 pm »
Yes understood. Thanks again for your help.

RNA structures (DSSR) / Re: DSSR issue --json and --analyze
« on: April 20, 2020, 11:32:50 am »
yes! thank you so much I did not realize that. That solves my problem. I didn't see that in the documentation.


RNA structures (DSSR) / Re: DSSR issue --json and --analyze
« on: April 20, 2020, 11:23:42 am »
Hi Xiang-Jun,

Thank you for your prompt response. I understand your point. This is just an ease of use feature. I can get everything I need by calling DSSR twice and parsing the old x3dna data via text. If you have time though I would love you to include the information from dssr-pairFrames.txt in your json dictionary under 'refFrames' that would be amazing. I am after both the origin and reference frame matrix.

I think you could accomplish this with the below format.

1 G1             C11            G-C WC           19-XIX    cWW  cW-W
        3.614304         2.453535        -9.939577      # origin
       -0.564447        -0.824117        -0.047238      # x-axis
        0.817888        -0.566084         0.102998      # y-axis
       -0.111623         0.019502         0.993559      # z-axis

would be

{'index' : 1, 'nt1' : 'G1', 'nt2': 'C11', 'bp' : 'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W',
'origin':  '3.614304         2.453535        -9.939577', 'x-axis': '-0.564447        -0.824117        -0.047238', 'y-axis' :  ' 0.817888        -0.566084         0.102998', 'z-axis' : ' -0.111623         0.019502         0.993559'}


RNA structures (DSSR) / DSSR issue --json and --analyze
« on: April 19, 2020, 11:20:27 pm »
Hi Xiang-Jun,

I must again commend you on your amazing software. Not only is it quite useful but you are incredibly responsive to issues.

I have downloaded your new version of DSSR and love the json support. I noticed though that if I use both --json and --analyze it will suppress the json output. It would be amazing if you can add in the --analyze info into the json.

x3dna-dssr -i=S_000001.pdb --json --analyze


General discussions (Q&As) / base pair frame from base frames
« on: February 26, 2014, 06:40:53 pm »
Hi Xiang-Jun,

I was hoping you could help me understand part of your tech_details.pdf. I was able to follow up to calculating the reference frame of each base and I am trying to understand how you combine them into "middle frame", presumably this is base pair frame? Shown on page 6 for base pair A_G1-B_C8.

Thank you very much.

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.