Messages

1

General discussions (Q&As) /

« 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!

Kevin

2

General discussions (Q&As) / 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!

Thanks,

Kevin

3

General discussions (Q&As) / thank you

« on: September 07, 2007, 02:47:40 pm »

Thanks for the speedy reply!

Well, I checked the example problem that you cited, and it appears to be reasonably similar to what I am seeing.  According to your reply, the ref_frames.dat file is exactly what I thought it was.  Thank you for your help,

Kevin

4

General discussions (Q&As) / question on reference frame (ref_frames.dat)

« on: September 06, 2007, 03:31:00 pm »

Hello,

First let me say that your program 3DNA is a wonderful gift to the scientific community!

I have a question about the reference frame used in your program, 3DNA.  

First, let me tell you a bit about my problem.  I am specifically interested in examining the Lac-R repressor and its structure when bound to known operator sequences.  The two segments of DNA contained in the .pdb file (1LBG.pdb) are largely distorted by the binding and appear to have a near 45 degree kink.  

My question is regarding the ref_frames.dat file.  When I look at my .pdb file and its interpretation of the DNA helix visually and overlay the ref frame returned by your program, the reference frame in the ref_frames.dat file seems to be contradictory to the helical structure.  Let me explain further.  While the coordinates returned in the ref_frames.dat file do appear to be in the "center" of the base pair, the reference frame gives a z-axis that does not appear to align with that of the DNA.  Also, the x-axis, which you say is supposed to point away from the minor groove, appears to be pointing in some other direction!  

My question is this: is the frame given in the ref_frames.dat file, the same as the one you refer to as the coordinate frame, where the positive x-axis is defined as pointing away from the minor groove?  If so, why do the axes appear to be pointing in these strange directions?  

I hope these inquiries make sense.  I was going to attach the .pdb, .out, and .dat files, but I cannot figure out how to do it!  If you care to reproduce my scenario, the pdb file is called "1LBG.pdb".  I simply ran

Code: [Select]

find_pair 1LBG.pdb stdout | analyze

Thank you in advance for your help, and I hope I have not carelessly missed something in the User's Manual!

Kevin Towles