Transformation of DNA keeping it's curvature constant

[mikeshelk]

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

[xiangjun]

Hi Mikhail,

Thanks for posting such an interesting question. As you guessed, the operation you'd like to make "may seem strange to some people". Indeed, I do not fully understand what you are trying to achieve, exactly. Could you use a simple, concrete example so others can see your point clearly? I am always interested in adapting 3DNA in ways that make sense to me and helpful to users like you.

Xiang-Jun

[mikeshelk]

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

[xiangjun]

Thanks for your clarification. It is certainly clearer. However, I am still confused how one could make base-pair movement while "keeping absolutely constant the backbone shape". Are you trying to make rigid body transformation; i.e., moving bp1 to bp2 while keeping the internal structure (base + backbone) unchanged? As suggested in my previous post, a simple/concrete/reproducible example would make your point unambiguous.

At this point, I do not think 3DNA has direct support to what you presumably want to do. However, if I could have a clear understanding of your question, I may be able to help in a more concrete way. Of course, always keep your mind open and try to explore other available tools.

Xiang-Jun

[mikeshelk]

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

Mikhail Schelkunov