Messages

1

General discussions (Q&As) / Rebuild from sugar-phosphate backbone

« on: October 30, 2010, 04:17:28 pm »

Hello, dear Xiang-Jun!

As far as I understood, "rebuild" builds structure from base parameters. So you wrote in your blog "The structural parameters can be used to rebuild the structure, which is virtually identical in base geometry (i.e., without taking consideration of the sugar-phosphate backbone) to the original structure"
Tell me please, is it possible somehow to rebuild structure using only sequence and sugar-phosphate backbone parameters? I.e. without time-consuming minimization to define approximately Calladine parameters for each nucleotide pair of a given sequence, having only backbone?

Thanks,
Mikhail Schelkunov

2

General discussions (Q&As) / What do numbers in *.inp files mean?

« on: August 25, 2010, 07:05:00 am »

Dr. Xiang-Jun, hello!
I would like to ask about the find_pair output
Consider a string "
  194  239  0 #    5 | -:...5_:[..T]T-----A[..A]:..23_:-  0.32  0.17 17.11  8.91 -0.83
"
Could you please tell me what all five numbers in "0.32  0.17 17.11  8.91 -0.83" exactly mean?

Thanks
Mikhail Schelkunov

3

General discussions (Q&As) / Re: Transformation of DNA keeping it's curvature constant

« on: August 25, 2010, 06:55:35 am »

Well, thank you a lot, Xiang-Jun, I suppose, I could do it by myself)

Mikhail Schelkunov

4

General discussions (Q&As) / Re: Transformation of DNA keeping it's curvature constant

« on: August 24, 2010, 08:14:53 am »

Dear Xiang-Jun,

I'll try to explain it easier.
Look at this picture

(http://picasaweb.google.com/lh/photo/pS ... directlink)
I would like to make some nucleotide movements, keeping absolutely constant the backbone shape (depicted in white).
For example, there is a basepair "1-1". I would like to move it a little bit left to the point "2-2". Also I want all other
nucleotides to move left by the same length. Is it possible to do this with 3DNA?

Thanks
Mikhail Schelkunov

5

General discussions (Q&As) / Transformation of DNA keeping it's curvature constant

« on: August 23, 2010, 02:20:37 pm »

Xiang-Jun, hello!

I would like to make an operation that may seem strange to some people.
I want to move a sugar-phosphate backbone keeping constant the total curvature of DNA. It means that the DNA structure will stay fixed, but the sugar-phosphate atoms (and all other atoms too, this can be made using "rebuild") should slide along it spirally. I would like to consider nonintegral shifts, for example 0.2, 0.4, 0.6 and 0.8 of P->P[i+1] length. How could I do this?
I suppose, I need to use an interpolation by splines for 3D-positions of atoms in a PDB-file to make intermediate structures, but I believe that I could do this a little bit easier with 3DNA. Could you please help me?

Thanks
Mikhail Schelkunov