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Messages - yrxin

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General discussions (Q&As) / I uploaded a 3DNA parser
« on: January 17, 2008, 09:33:15 pm »
Hi Xiangjun and members on this forum,

I uploaded a 3DNA parser to User's Contribution. You are welcome to test and give me feedback.



Users' contributions / 3DNA parser
« on: January 17, 2008, 09:30:21 pm »

I wrote a python package to parse PDB and 3DNA output files.

Briefly speaking of this package, it reads PDB files to get structure information, such as atom, residue. It then reads output files generated by "find_pair -p" and "find_pair | analyze" to get base-pairing, base-stacking, and helical information. I have a "manual" folder showing a couple of examples.

Any kind of comments are welcome.


General discussions (Q&As) / parameters to define quasi-continuous helix
« on: November 16, 2007, 11:27:22 am »
Hi Xiangjun,

I have a question about quasi-continuous helix. How does 3DNA define a "helix"? I found a couple of parameters, but was wondering if there is any other parameters. I am listing the parameters I found and some brief explanation. Please correct me and add more parameters if any.

1. helix_break: the distance between origins of two base pairs
2. std_curved: to decide if the helix is curved. (what does it mean?)

Thank you very much,


General discussions (Q&As) /
« on: October 27, 2007, 01:41:54 pm »
Hi Mauricio,

I think the poc_haxis.r3d file may be related to the curve of the helix as it is commented in the file. If the helix is not strongly bent, you will get this r3d file after running analyze. The helix could be a conventional or a quasi-continuous one. However, I don't exactly know the numerical criteria of the bend. Is it related to the parameter "std_curved"? I am sure Xiang-Jun knows it very well, and he may answer the question better.

Xiang-Jun, could you please help to explain it? Thank you.


General discussions (Q&As) /
« on: October 09, 2007, 10:04:24 am »
Thank you, Xiangjun.

I am glad that you fixed it, and I will be more than happy to report a bug.


General discussions (Q&As) / A find_pair problem
« on: October 08, 2007, 08:14:14 am »

I used "find_pair -p" to analyze rr0027. There is one strange base pair.

    41    2   38  529 ....>A:..39_:[..G]G-**+-A[..A]:.530_:A<....
             G+A    -10.06    3.90    1.74   11.86  -27.77 -155.28
             G+A [4] 0µ^E
                    parallel trans trans
            --+    153.3    143.1     30.2    143.4   -173.2   -116.3
        10.92    1.74   30.20    6.73   15.91   70.79  132.87  182.56

I don't know what the string "0µ^E" mean. It is supposed to be hydrogen bond information there.

I was wondering if there is a bug. Thank you.

By the way, I used v2.0.

General discussions (Q&As) / The windows and mac versions of 3DNA
« on: September 24, 2007, 03:23:02 pm »
Hi Xiangjun,

I was wondering if you could provide a windows version of 3DNA v2.0 (mac version is also good). Thank you very much.

General discussions (Q&As) / models in a structure
« on: September 24, 2007, 11:51:12 am »
Hi Xiangjun,

I used v2.0 to analyze ar0062. This structure has two models and 3dna can only find base pairs of model 1. I found that the difference between the two models is the alternative location.
Model 1:
ATOM      1  O5*A  C A   1   .....

Model 2:
ATOM      1  O5*C  C A   1   .....

In the 'misc_3dna.par' file, there is a line related to alternative location: alt_list: A1. How can I change this line in order to find base pairs in model 2.



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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.