Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Author Topic: ref frames question  (Read 8145 times)

Offline kbt22

  • with-posts
  • *
  • Posts: 2
    • View Profile
ref frames question
« on: October 09, 2007, 09:59:08 am »
I asked a question about a month or so ago regarding the ref_frames.dat file.  In fact, I think I have discovered my original problem, and I thought it useful to report it here.

Please correct me if I am wrong!!! The notation in the ref_frames.dat file was actually the transpose of what I thought! I would typically notate a 3d reference frame as follows:

[a11, a12, a13]  <- X Components of Axis Vectors
[a21, a22, a23]  <- Y Components of Axis Vectors
[a31, a32, a33]  <- Z Components of Axis Vectors

i.e. the x-axis vector is composed of elements [a11, a21, a31]

However, it appears from your file that the ref_frames.dat is actually the transpose of this!  That is why I originally reported that the frames "appear to be pointing in unusual directions!"  Let me clarify... The ref_frames.dat file instead outputs

[a11, a12, a13] <- X Axis Vectors
[a21, a22, a23] <- Y Axis Vectors
[a31, a32, a33] <- Z Axis Vectors

i.e. the x-axis vector is composed of elements [a11, a12, a13]

Is that right? If so, did I miss somewhere that this is explicitly stated?  I am used to using a different convention!



Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1640
    • View Profile
    • 3DNA homepage
(No subject)
« Reply #1 on: October 09, 2007, 11:01:05 pm »
Hi Keven,

Thank  for reporting your explorations on the x-, y-, and z-axis direction convention adopted in the "ref_frames.dat" file generated with 3DNA.

Firstly, I like the clarity and completeness you pose this question: it serves as an example for most others to follow in asking questions, not only in the 3DNA forum, but also in a more general context.

Secondly, you are right in figuring out that
Quote from: "Keven"
the x-axis vector is composed of elements [a11, a12, a13]

As you can imagine, this feature is not documented (neither are many other features, as a matter of fact). From the very beginning, I had anticipated that some users would be able to take advantage of this file as they dig more deeply into 3DNA. In fact, this reference frame file is generated by several programs from 3DNA. It is mostly used internally by the utility "frame_mol", and I have never been asked for clarification. You are the first user (I know of) who has checked into such technical details.

Thirdly, as a response to your question, I have modified the source code of 3DNA  (for future release, v2.0) and the file now reads as follows:
Code: [Select]
...     1 C-G ...
   17.1274    25.9624    25.8783  # origin
   -0.9873     0.1544     0.0378  # x-axis
    0.1215     0.8864    -0.4467  # y-axis
   -0.1025    -0.4365    -0.8939  # z-axis

Does this clarify the issue? What text would you suggest to make its meaning more explicit?


« Last Edit: October 10, 2007, 07:57:40 pm by xiangjun »

Offline kbt22

  • with-posts
  • *
  • Posts: 2
    • View Profile
(No subject)
« Reply #2 on: October 10, 2007, 06:25:29 pm »
Hi Xiang-Jun,

Thanks for the comments.  I think the additions to the code notating the axes are very helpful.  That would be more than adequate explanation in my opinion.

I didn't even think to question the format of the numbers initially; rather, I jumped right in.  Only after I was sure that the way I had it couldn't be right, did I figure it out!  In a moment of clarity, I realized that it could be a notation difference.  I took the tranpsose and voila!  

Thanks again for your useful program!



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