Messages

1

w3DNA -- web interface to 3DNA / Re: Is w3DNA down?

« on: July 01, 2015, 02:53:41 pm »

We are working on the issue now.  I hope to have the server up shortly.  I will post here once the problems is resolved.

2

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

3

General discussions (Q&As) / Re: Individual Model images in x3dna_ensemble block_image

« on: October 14, 2013, 10:54:10 am »

Thank you, the description of the -v option being shorthand for other options helped.

As far as ensemble output being as expected, I understand that.  I guess a feature request would be a command line opting to produce an r3d file for each model without the need to use ex_str to break the models into individual files and then blockview on each structure to generate the image, for now I will wrap those commands in a script.

Thanks for your help.

Andrew

4

General discussions (Q&As) / Re: Individual Model images in x3dna_ensemble block_image

« on: October 08, 2013, 02:09:40 pm »

Also,

What is the difference between the following

x3dna_ensemble reorient -r "b" -e  in.pdb -o out_reorient_b.pdb

which uses the best principal axis of base atoms from the rotate_mol command

and
x3dna_ensemble reorient -v -e in.pdb -o out_reorient_e.pdb

which uses the the "best view" from the reorient command.  If I open the images together they are very similar.

Thanks

Andrew

5

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

6

General discussions (Q&As) / Protocol 3 - Construction of a DNA Structure

« on: August 12, 2013, 11:07:55 am »

Please post questions related to Protocol 3 in this thread.

7

General discussions (Q&As) / 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.

8

General discussions (Q&As) / 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-v2.1and 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.

9

General discussions (Q&As) / 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

10

w3DNA -- web interface to 3DNA / Re: Protein Bound DNA via w3DNA

« on: June 04, 2013, 12:31:35 pm »

When using the reconstruction section of the w3DNA website to create protein bound DNA the following method applies

-  DNA base pairs interacting with protein in the original X-ray will adopt the same configuration (pair and step parameters) as those found in the original structure.  Because of this the model must have at a minimum the same number of steps as found in the X-ray structure.

- Extra DNA that you add to the beginning or end of the structure will adopt the configuration (A-, B-) selected on the w3DNA site.

If I did not answer your question please let me know so that I can further assist you.

Thanks,

Andrew

 

11

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?

12

Feature requests / Re: Align multi-model (NMR) structures

« on: February 01, 2012, 12:08:19 pm »

Hi XJL,
  The program works great on NMR type MODEL/ENDMDL structures but doesn't have the same features as the ensamble_analyzes with the availability to run on a collection of files with a -l fileList option.  Would it be difficult to add this feature so that on can align on both a multi-model pdb or a set of seperate pdb files?

Thanks
Andrew

13

Feature requests / Re: Align multi-model (NMR) structures

« on: December 30, 2011, 12:07:21 pm »

Before I can get something for an "official" release of 3DNA v2.1 with this new feature included, I will try to come up with a Ruby script this week for you to try out.

Now to a specific point related to the procedure your outlined:

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.

As with the MD simulation analysis script ('x3dna_md.rb'), it would be best for a user to specify the base pairing information. Thus the program 'find_pair' does not need to be run with each model. This would ensure consistency in all the models. Instead, the model-specific 'ref_frame.dat' can be generated with 'analyze'.

True, analyze can provide the ref_frame.dat.  I looked into using nmr_strs which runs analyze on each structure but it overwrites the ref_frame.dat file on each model.  You may be able to modify nmr_strs to take rotate_mol as an input, but a standalone ruby script would also work, whatever you think is best.

Andrew

14

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.