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### Topics - acolasanti

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##### RNA structures (DSSR) / negative stretch and opening in RNA pairs
« on: March 07, 2014, 12:59:51 pm »
Hello,

I have a question regarding base-pair parameter calculations with DSSR.  I was analyzing some RNA structures and looking at a specific base-pair type, the G+A : tm+m pair (and A+G :tm+m).  These pairings usually fall withing higher pairing patterns (ie triplet pairs).  I was expecting that I would be able to 'flip' the A+G over to look like the G+A, ie taking - shear and buckle, and this is correct.  What I was not expecting was negative values of stretch and opening in G+A vs positive in the A+G.

Here is an example output

Pair 1 is A+G in 3SDS
7 1:A.A8           1:A.G44          A+G              00-n/a    tSS tm+m
7    1    8   44 ....>A:...8_:[..A]A-**+-G[..G]:..44_:A<....
A+G      3.21    8.15   -0.00  -19.59    0.27  175.33
A+G [1]  N3 - N2  3.15
parallel trans trans

Pair 2 is G+A in 4ENB
3 1:A.G3           1:A.A21          G+A              00-n/a    tSS tm+m
3    2    3   21 ....>A:...3_:[..G]G-**+-A[..A]:..21_:A<....
G+A     -2.55   -7.43    0.59  -25.28    0.52 -148.92
G+A [2]  O2'- N1  2.61  N2 - N3  3.12
parallel trans trans

Both of the pairs overlap well in 3D space.  I was also to see the orientation of both pairs the same in the dssr-pairs.pdb file, I thought the G+A and G+A would be rotated 180deg with respect to each other but both were in the same orientation.

Can you tell me the meaning of the negative parameters?  Should I expect these in other pairings?  I am used to DNA analysis with 3DNA-analyze and in that case an A-T pair and a T-A pair are the same except for movement along the x-axis.

Thanks,

Andrew

2
##### General discussions (Q&As) / Individual Model images in x3dna_ensemble block_image
« on: October 08, 2013, 01:02:27 pm »
Hello,

I am using the x3dna_ensemble program to process NMR and multi model structures.  When I use block_image I get as output a pdb and r3d of the entire ensemble, is it possible to get r3d output for each model using this method?

Thank you

Andrew

3
##### JoVE / Protocol 3 - Construction of a DNA Structure
« on: August 12, 2013, 11:07:55 am »

4
##### JoVE / Protocol 2 - Analysis of a Crystal Structure
« on: August 10, 2013, 03:28:31 pm »
In this protocol the structure 2NP2 was used.

Information about the structure can be found at the RCSB with the following link http://www.rcsb.org/pdb/explore.do?structureId=2np2.

The pdb structure file is attached.

5
##### JoVE / Protocol 1 - Install Instructions of 3DNA on a Mac
« on: August 10, 2013, 03:17:10 pm »
In order to install the 3DNA software package on a Mac you must first register for the 3DNA forum, this will give you access to the Downloads section found on the main forum page.  If you are not registered or are visiting as a guest and not logged in you will not have access to the Downloads section.

Once you have registered for the forum and downloaded the appropriate software package  you will need to unpack the tar.gz file, which is accomplished by double-clicking on the compressed file.  This will create a folder named x3dna-v2.1 which contains all of the needed software files.  This folder can be moved to any location on your system, in the Jove paper we move it to the 'Applications' directory.

After unpacking the software and moving it to an appropriate location you will need to open a terminal window to complete the install.  Once in a terminal window change to the directory which contains the 3DNA software, Applications in our case, with the following command:
Code: [Select]
`cd /Applications/x3dna-v2.1`and run the setup script by typing
Code: [Select]
`./bin/x3dna_setup`
The setup script will print information about the software to the monitor.  You will need to follow the instructions printed and paste the lines into your resource file, .bashrc if you are running a bash environment or .tcshrc if you run a tcsh environment. Note that the type of environment will also be printed when you run the setup script.

You can use TextEdit or another text editing application to add the environmental variables to your resource file.  Make sure that you are saving as pure text.  In TextEdit this is done by selecting 'Make Plain Text' from the format menu.

Once you have edited and saved your resource file you need to apply the changes.  This only has to be done when you change the file, not every time you want to use the 3DNA software.   You can type source ~/.bashrc or source ~/.tcshrc depending on your system or you can close and open the terminal.

3DNA should now be installed and ready to use.

6
##### JoVE / Jove Questions and Supplimental Files
« on: August 09, 2013, 05:11:25 pm »
Please ask general questions about the Jove paper in this section of the forum.  I will set up a topic for each Protocol section, please put questions or comments in the appropriate place for ease of reference.

Thank you,

Andrew Colasanti

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##### w3DNA -- web interface to 3DNA / Protein Bound DNA via w3DNA
« on: June 04, 2013, 12:30:30 pm »
This question arrived via email :

I have a question regarding the reconstruction of a protein-bound DNA model from Web 3DNA.
When I use this function to create a complex of a protein bound to a DNA duplex, is the DNA structure (and the protein structure) locally distorted by the interaction?

8
##### Feature requests / Align multi-model (NMR) structures
« on: December 28, 2011, 04:17:37 pm »
I know that 3DNA has some commands for multi-model NMR files such as nmr_ensemble  for visualization and nmr_strs  for analysis.  I have a suggestion on a new feature for multi-model NMR files, some sort of alignment command to align on each model's reference frame.  I performed this by hand as an example using the following

- Split the multi-model file into individual pdb files, 1 for each model
- for each model...
- find_pair on the structure
- rotate_mol using the ref_frame.dat file from find_pair

The pairing is consistent in all of the models but we have to run find_pair on each structure in order to get the reference frame data.  I have attached 2 images to the example.

2KEI_org_v1 shows the structures framed on Base pair 1 of model 1, the other models are kept in the same relation to this model as they were in the original pdb file (probably some sort of Ca rms).  I rotated the structures 90deg about BP1 minor groove for better visualization.

2KEI_fr1_v1 shows each model aligned on its base pair frame 1, we can see how the other end of the DNA changes if we hold the first pair fixed.

I rotated the structures 90deg about BP1 minor groove for better visualization.

I know that a short python/ruby script can be written to do this but thought it would be a nice feature for the official 3DNA package.

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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.