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Author Topic: A find_pair problem  (Read 8527 times)

Offline yrxin

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A find_pair problem
« on: October 08, 2007, 08:14:14 am »
Xiangjun,

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.

Offline xiangjun

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« Reply #1 on: October 08, 2007, 09:37:28 pm »
Hi Yurong,

Thanks for reporting the case: it is indeed a bug. I have fixed it and committed the change to the code base of 3DNA v2.0. Before I have the time to produce an updated binary of v2.0 for users to try out, you can simply ignore it, or set H-bonding distance cut-off to 3.5 A instead of 4.0 A with the "-p" option. I will let you know when I have a new compiled version for Linux/Mac OS X/Cygwin etc.

FYI, the bug was due to a very special case where a character string was not initialized. The program produced that garbage string where it should have been empty.

Keep in mind that, to me, the more bugs you report, the merrier! 3DNA becomes more robust by fixing bugs ...

Xiang-Jun

Offline yrxin

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« Reply #2 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.

Yurong

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.