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Author Topic: Elongate RNA pdb structure  (Read 923 times)

Offline remba87

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Elongate RNA pdb structure
« on: January 30, 2018, 05:11:20 am »
Hello,
I would like to elongate some RNA pdb structures from my simulation...
I would like to add some C-G base pair in order to make the molecule longer to simulate the SAXS curves.
I tried to look in the forum, but I did not find anything...
any suggestion?
Thanks for the help

Luca

Offline xiangjun

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Re: Elongate RNA pdb structure
« Reply #1 on: January 30, 2018, 09:48:36 am »
Hi Luca,

Thanks for using 3DNA and for posting your question on the Forum.

I vaguely understand what you want to achieve. Have a look of the following two threads:


It would help if you are specific by using a concrete example.


As a side note, you do not need to post the same question more than once in different sections of the Forum. I’ve removed one of them, and move the remaining one to the more relevant section http://forum.x3dna.org/general-discussions/

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline remba87

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Re: Elongate RNA pdb structure
« Reply #2 on: January 30, 2018, 11:07:36 am »
I try to be more clear... I have a MD simulation of my RNA system...it has 25 nucleotides then it has a bulge in the middle (U7). What I want to observe is the differences of the overall structures between the U7 inside the double helix, and the U7 outside from the double helix. we think that this difference mean a different angle of the helix. So we did SAXS experiments to measure that difference but we did not see anything different. this is probably due to the size of the RNA (too small).
Before make other SAXS experiments we want to make a theoretical study of the predicted SAXS curves so we would like to see at which length of the RNA we are able to observe some differences in the saxs curves. So I would like to elongate 2 RNA structures (in and OUT) obtained from a MD simulation. So I would like to add some base pairs at the bottom of the RNA and also after the bulge (that is in the middle of the RNA)

I hope I made more clear my problem, Anyway now I start to see what you suggested me.

Thanks for the help

Luca

Offline xiangjun

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Re: Elongate RNA pdb structure
« Reply #3 on: January 30, 2018, 11:16:17 am »
Hi Luca,

3DNA does not have a 'straightforward' way to address your questions. However, as shown in the two links in my previous response, some of the 3DNA programs combined could do the trick. I'd help as much as practical.

Alternatively, there are numerous other DNA/RNA modeling programs that may better fit your needs.

Xiang-Jun 
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.