Messages

1301

Site announcements / The forum is shaping up nicely

« on: April 24, 2012, 03:09:31 pm »

Ever since new 3DNA forum was made public in early March, it is shaping up quite nicely. As demonstrated by the statistics, the number of registrations and posts have increased significantly thereafter. The following table is a snapshot of the section "Forum History (using forum time offset)" (at the bottom of the statistics page) as of today while I am writing this post:

Yearly Summary     New Topics  New Posts   New Members   Most Online
 2012                  39          163          114            11
    April 2012         7           60           44             9
    March 2012         13          55           61             11
    February 2012      13          38           7              6
    January 2012       6           10           2              6
 2011                  3           6            8              6

Note that most of the posts in February were composed by myself in preparing the forum for public release.

As made clear in my initial welcome message, the forum was created to make 3DNA-related discussions archived, searchable, and viewable to the public (without registration). With support from the community at large, enthusiastic users in particular, 3DNA forum is functioning well as expected -- thank you! As 3DNA enjoys wider recognition it deserves, the forum is more than likely to become more active, and potentially turns into "an online community for DNA/RNA structural bioinformatics."

I'd like to emphasize again that any 3DNA-related questions are welcome and should be directed to this 3DNA forum. As always, I strive to provide a prompt and concrete response to each and every question posted here. No email or private forum message, please -- by asking your questions on the public 3DNA Forum, you are benefiting not only yourself but also the whole user community.

Xiang-Jun

1302

General discussions (Q&As) / Re: Missing files from analyze?

« on: April 23, 2012, 10:48:14 pm »

Glad to see "it worked beautifully". So 3DNA is not that hard to pick up.

I just "chopped up" my RNA, isolating the helix I was interested

Just curious, what do you mean by "chopping up" your RNA? Did you know that the default settings of find_pair automatically locate all double helical regions in an RNA structure, and store the fragments in file "hel_regions.pdb"? Does this functionality help?

Prompted by you initial question, I am considering to refine the "analyze" program to output "stacking.pdb" for single-stranded DNA/RNA structures as well. This is yet another example of how a user's question helps improve 3DNA.

Xiang-Jun

1303

General discussions (Q&As) / Re: Missing files from analyze?

« on: April 23, 2012, 04:49:43 pm »

Welcome to 3DNA!

Are you using the "-s" option [for single-strand (ss)] with your RNA structure? In its current setting, 3DNA generates the "stacking.pdb" file only for a duplex. I will consider adding "stacking.pdb" for ss-DNA/RNA if it's useful to you -- so far, you're the only 3DNA user having this "problem", if I understand your post correctly.

Xiang-Jun

1304

Feature requests / Re: Mutate_Bases: Option to mutate all residues of the same type to another

« on: April 20, 2012, 11:05:59 am »

Thanks for your request for adding new options to mutate_bases "to mutate all residues of the same type to another". I see your point, but I feel such functionality is better served by purpose-specific scripts instead of by mutate_bases itself. As a general design principle, I aim to make the core part of 3DNA focused, robust and efficient, and use Ruby scripts to build up features of general interest. Overall, 3DNA is intended as a toolset to be used as users see fit.

With regard to mutate_bases, I am considering to add an option to list all bases (nucleotides) in a PDB structure in a format that can be easily modified (either manually or pragmatically) and then fed back to the program. This option allows for easy adaptation of mutate_bases to various common situations (including yours), without adding too many bells and whistles that would blur the program's primary function.

An excerpt example for the first 12 bases of 6tna is as below:

Code: [Select]

chain=A snum=1 name=G
chain=A snum=2 name=C
chain=A snum=3 name=G
chain=A snum=4 name=G
chain=A snum=5 name=A
chain=A snum=6 name=U
chain=A snum=7 name=U
chain=A snum=8 name=U
chain=A snum=9 name=A
chain=A snum=10 name=2MG
chain=A snum=11 name=C
chain=A snum=12 name=U
Does this sound useful?

Xiang-Jun

1305

General discussions (Q&As) / Re: local helical axis

« on: April 20, 2012, 09:44:21 am »

In my previous reply, I asked you if the "Position (Px, Py, Pz) and local helical axis vector" from analyze output file are what you want. From my understanding of your question "Where can I find the vectors of the local helical axis?", I guess they should be. Please confirm.

The "ref_frames.dat" file, as its name implies, contains the reference frames of all base pairs.

Xiang-Jun

1306

RNA structures (DSSR) / Re: Single-Stranded Based Zp Parameter

« on: April 19, 2012, 05:21:58 pm »

Yes, the -torsion option of analyze is intended to be standalone, starting directly from a PDB file, without first running find_pair. The "-c" option does not apply here and is silently ignored.

As I mentioned in several occasions, all nucleic acid backbone torsion angles can be calculated as follows (using 6tna as an example, and the output file would be in '6tna.outs'):

Code: [Select]

find_pair -s 6tna.pdb 6tna.nts
analyze 6tna.nts

# or the above two commands can be combined:
find_pair -s 6tna.pdb stdout | analyze stdin
This functionality has been there since 3DNA v1.5, but it is not widely recognized/used by the community. Once in a while, I notice from literature (mostly on RNA structures) some sort of ad hoc scripts to calculate just those torsion angles.

Now by adding this -torsion option explicitly, by cutting one extra step, and by providing more useful features, I am hoping the new "analyze -torsion" combo would gradually find its way in RNA structure related research.

As always, I am open to suggestions to continuously refine this new feature of 3DNA.

Xiang-Jun

1307

General discussions (Q&As) / Re: local helical axis

« on: April 19, 2012, 03:31:20 pm »

Does the section (from analyze output) as below fit the bill? Here I am using 355d/bdl084 as an example.

Code: [Select]

Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
         for each dinucleotide step

     step       Px        Py        Pz        Hx        Hy        Hz
   1 CG/CG     15.99     26.43     24.17      0.03     -0.21     -0.98
   2 GC/GC     17.37     23.05     21.31     -0.39     -0.41     -0.82
   3 CG/CG     15.84     24.53     17.27      0.23     -0.39     -0.89
   4 GA/TC     15.59     22.51     14.84     -0.16     -0.35     -0.92
   5 AA/TT     15.65     20.84     11.86     -0.14     -0.31     -0.94
   6 AT/AT     15.26     20.22      8.64     -0.14     -0.22     -0.97
   7 TT/AA     15.05     19.77      5.44     -0.12     -0.30     -0.95
   8 TC/GA     14.55     19.21      2.15     -0.12     -0.26     -0.96
   9 CG/CG     11.86     20.64     -0.66     -0.23     -0.04     -0.97
  10 GC/GC     14.37     17.46     -3.79     -0.05     -0.38     -0.93
  11 CG/CG     12.05     18.00     -7.38     -0.08      0.04     -1.00

Xiang-Jun

1308

RNA structures (DSSR) / Re: Single-Stranded Based Zp Parameter

« on: April 19, 2012, 03:11:03 pm »

Hi,

Thanks for your quick catch -- I am planning to write a post talking about these new parameters :-).

Okay, the new option is -torsion (can be abbreviated to -t) for the analyze program. It is meant to be easy to use, efficient, and robust for real-world applications. As always, the point is best illustrated with concrete examples -- do the following and then check output files '1jj2.tor' and '6tna.tor':

Code: [Select]

analyze -t=1jj2.tor 1jj2.pdb
analyze -torsion=6tna.tor 6tna.pdb
Try to delete base atoms, some of backbone atoms, or use a PNA structure etc, the program should behave properly. I'd like to hear your feedback on how the program is working ...

Xiang-Jun

1309

MD simulations / Re: Analysis of PDB file:query

« on: April 19, 2012, 12:18:08 pm »

now got 14 nos. of base pairs out of 15

There must be something special with the missing base pair. If you visualize the structure graphically using Jmol/PyMOL etc, I believe you won't take it as a "base pair" either. Checking the details why it is "missed" by find_pair would be an interesting exercise for those who want to understand 3DNA better.

Xiang-Jun

1310

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 19, 2012, 07:54:44 am »

From the information you provided, 3DNA is clearly not properly setup in your Windows system. I was confused how you could run find_pair etc.

You said you used the compiled version of 3DNA for MinGW/MSYS, so why not you launch a MinGW Shell?

C:\Users\triindia>cd C:\X3DNA\3DNA bin

You have a directory named 3DNA bin? A space between 3DNA and bin?

In my MinGW Shell, this is the output from 3DNA v2.1beta setup script.

$ x3dna-v2.1beta/bin/x3dna_setup
Unknown shell: not-set -- you've to set X3DNA and PATH manually:
             o set up the X3DNA environment variable
             o add $X3DNA/bin to your command search path
Setting up 3DNA should be a straightforward process. If you have
technical problems, ask a local expert for help, or post them at
the 3DNA forum.

I installed 3DNA under directory $HOME/x3dna-v2.1beta. So I have created a text file (named set-me-up), with $X3DNA environment variable and X3DNA/bin path set explicitly as below:

Code: [Select]

export X3DNA=$HOME/x3dna-v2.1beta
export PATH=$X3DNA/bin:$PATH
Then I can run the following (note it is a dot at the beginning):

Code: [Select]

. set-me-up
and you will see the following when run the "blocview -h" command:

~ [237] blocview -h
===========================================================================
SYNOPSIS
    blocview [OPTION]... PDBFILE
DESCRIPTION
    Generates a schematic image which combines base block representation
    with protein ribbon. The image has informative color coding for the
    nucleic acid part and is set in the "best-view" by default. Users need
    to have MolScript, Raster3D and ImageMagick properly installed on their
    system.
        -o   use original coordinates contained in the PDB data file
        -j   output image in JPG format (default to PNG)
        -t[=]RESOLUTION   create PyMOL ray-traced image at RESOLUTION
        -d   display the generated image using "display" of ImageMagick
        -b   ball and stick model with filled base ring
        -c   clean up temporary common files
        -r   only backbone P atoms + base Ring atoms of nucleic acids
        -p   set the best view based on Protein atoms
        -a   set the best view based on All atoms
        -s[=]NUM    set scale factor for the image
        -i[=]IMAGE  set image file name (default to t.png)
        -x|y|z=ANGLE  rotation around x, y, or z-axis by ANGLE degrees
        PDBFILE   a PDB data file name (other than 't.pdb')
EXAMPLES
    blocview -d -i=bdl084.png bdl084.pdb
AUTHOR
    3DNA v2.0 [June 8, 2008] (by Dr. Xiang-Jun Lu; 3dna.lu@gmail.com)
    Check URL: http://x3dna.org/ for the latest
===========================================================================

If the instruction still does not make sense to you, your best bet may be to consult a local expert for setting up 3DNA. Alternatively, you can try w3DNA: the web-interface to commonly used functionality of 3DNA.

Xiang-Jun

1311

MD simulations / Re: Analysis of PDB file:query

« on: April 18, 2012, 09:33:32 am »

Okay, let's check step-by-step how find_pair is working for your two attached structures.

• The output for 30ns@mod_2.pdb is as you expected.
  

  find_pair 30ns@mod_2.pdb 30ns@mod_2.bps
  more 30ns@mod_2.bps
  # the output is as below
  30ns@mod_2.pdb
  30ns@mod_2.out
      2         # duplex
     14         # number of base-pairs
      1    1    # explicit bp numbering/hetero atoms
      1   31  0 #    1 | ....>-:...1_:[DA5]a-**--t[TPN]:..31_:-<....  4.71  1.82 45.14  7.30  7.61
      2   30  0 #    2 | ....>-:...2_:[.DA]A-----t[TPN]:..30_:-<....  0.51  0.30 13.22  9.70 -3.24
      3   29  0 #    3 | ....>-:...3_:[.DT]T-----a[APN]:..29_:-<....  0.73  0.73  8.66  9.13 -2.38
      4   28  0 #    4 | ....>-:...4_:[.DT]T-----a[APN]:..28_:-<....  0.19  0.09 13.10  9.21 -3.98
      5   27  0 #    5 | ....>-:...5_:[.DT]T-----a[APN]:..27_:-<....  1.03  1.03 17.68  8.93  0.96
      6   26  0 #    6 | ....>-:...6_:[.DT]T-----a[APN]:..26_:-<....  0.23  0.22 16.23  9.13 -3.52
      7   25  0 #    7 | ....>-:...7_:[.DT]T-----a[APN]:..25_:-<....  0.37  0.36 10.91  8.99 -3.36
      8   24  0 #    8 | ....>-:...8_:[.DT]T-----a[APN]:..24_:-<....  0.30  0.01  9.28  9.21 -4.21
      9   23  0 #    9 | ....>-:...9_:[.DT]T-----a[APN]:..23_:-<....  0.49  0.12 10.87  9.24 -3.73
     10   22  0 #   10 | ....>-:..10_:[.DT]T-----a[APN]:..22_:-<....  0.18  0.05 14.36  8.97 -4.00
     11   21  0 #   11 | ....>-:..11_:[.DA]A-----t[TPN]:..21_:-<....  0.47  0.21  1.26  9.28 -4.05
     12   20  0 #   12 | ....>-:..12_:[.DT]T-----a[APN]:..20_:-<....  0.34  0.30  5.05  9.10 -3.80
     13   19  0 #   13 | ....>-:..13_:[.DT]T-----a[APN]:..19_:-<....  0.46  0.45 22.22  8.98 -2.53
     14   18  0 #   14 | ....>-:..14_:[.DT]T-----a[APN]:..18_:-<....  0.47  0.28 25.44  9.34 -2.71
  ##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
  ##### 1 non-Watson-Crick base-pair, and 1 helix (0 isolated bps)
  ##### Helix #1 (14): 1 - 14  ***broken O3' to P[i+1] linkage***
  

  Using Jmol/PyMOL/RasMol to visualize the structure, one can easily verify that find_pair is behaving properly.
• Now repeat the procedute for 30ns_nsp_mod.pdb, you'd get the following result which you thought as "improper":
  

  find_pair 30ns_nsp_mod.pdb 30ns_nsp_mod.bps
  more 30ns_nsp_mod.bps
  # the output is as below
  30ns_nsp_mod.pdb
  30ns_nsp_mod.out
      2         # duplex
     10         # number of base-pairs
      1    1    # explicit bp numbering/hetero atoms
      1   31  0 #    1 | ....>-:...1_:[..A]A-**--T[..T]:..31_:-<....  6.27  0.03 22.42  9.06  6.46
      2   30  0 #    2 | ....>-:...2_:[..A]A-**--T[..T]:..30_:-<....  4.14  0.42 23.12  9.56  5.13
      3   29  0 #    3 | ....>-:...3_:[..T]T-----A[ADE]:..29_:-<....  0.13  0.01 20.45  9.45 -3.83
      4   28  0 #    4 | ....>-:...4_:[..T]T-----A[..A]:..28_:-<....  0.28  0.28 19.08  9.01 -3.21
      5   27  0 #    5 | ....>-:...5_:[..T]T-----A[..A]:..27_:-<....  0.40  0.11 18.15  9.35 -3.47
      6   26  0 #    6 | ....>-:...6_:[..T]T-----A[ADE]:..26_:-<....  0.64  0.51 27.99  9.05 -1.94
      7   25  9 #    7 x ....>-:...7_:[..T]T-----A[..A]:..25_:-<....  0.62  0.56 25.16  9.15 -2.00
     10   22  1 #    8 + ....>-:..10_:[..T]T-----A[..A]:..22_:-<....  0.64  0.53 15.83  9.01 -2.50
     13   19  0 #    9 | ....>-:..13_:[..T]T-----A[ADE]:..19_:-<....  0.48  0.19 18.51  5.17 -3.21
     14   18  0 #   10 | ....>-:..14_:[..T]T-----A[..A]:..18_:-<....  0.27  0.26 30.07  4.91 -2.71
  ##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
  ##### 2 non-Watson-Crick base-pairs, and 3 helices (1 isolated bp)
  ##### Helix #1 (7): 1 - 7  ***broken O3' to P[i+1] linkage***
  ##### Helix #2 (1): 8
  ##### Helix #3 (2): 9 - 10  ***broken O3' to P[i+1] linkage***
  

  As shown in the image below, find_pair is again behaving as it should for this case. Is this structure itself what you'd expect?
  
  
  

In my experience, whenever a user suspects the output from find_pair as "improper", it is more than likely that the structure itself is "weird" -- if in doubt, always check your structure using a molecular graphics visualization program (Jmol/PyMOL/RasMol etc). Of course, I am consistently on the watch to refine find_pair, especially for the edge cases.

Xiang-Jun

1312

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 17, 2012, 11:10:49 am »

Thanks for providing your system info (MinGW/MSYS). The error message means either you do not have 3DNA installed properly, or the script blocview is not executable. Which version of 3DNA are you using?

Do the following and report back verbterm the output:

Code: [Select]

cd $X3DNA/bin
ls -al
Xiang-Jun

1313

MD simulations / Re: Analysis of PDB file:query

« on: April 17, 2012, 11:04:14 am »

I found the output files were not proper

What do you mean "not proper"? What would you expect the output to be? I tried your attached PDB files, and found 3DNA is doing its job.

Xiang-Jun

1314

MD simulations / Re: How to properly use x3dna_ensemble?

« on: April 16, 2012, 05:08:57 pm »

Hi Nikolay,

Check the updated version dated 2012apr16 on the download page, and let me know if you have any problem.

Xiang-Jun

1315

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 16, 2012, 03:11:20 pm »

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

It is a bit complicated to setup the environment to run blocview (especially on Windows), for two reasons:

• It is a Perl script, so you need to have Perl installed on your Windows system.
• The script calls various 3DNA components, and third-party tools including MolScript, render in Raster3D, convert of ImageMagick. See the 2008 3DNA 3DNA Nature Protocols paper for details.

You may be able to run blocview using Cygwin on Windows, but I've never tried it myself. Any comments from other users? In my experience, it is straightforward to use blocview on Linux or Mac OS X where such third-party components are readily available. In future releases of 3DNA (presumably starting from v2.2), blocview would alternatively take advantage of PyMOL.

Now back to your question, are you using MinGW/MSYS or Cygwin? Please give details about the error message, using copy-and-paste.

Xiang-Jun

1316

MD simulations / Re: Analysis of PDB file

« on: April 07, 2012, 09:21:16 am »

Hi,

The simple Perl script manalyze was introduced around v1.5 for the analysis of "multiple" structures. Over the years, I've not been aware of its usage: your question is the first one. As of v2.1beta, I am migrating from Perl to Ruby as the scripting language for 3DNA. Now manalyze and most other not widely used Perl scripts are moved out the $X3DNA/bin/ directory into $X3DNA/perl_scripts/ -- they are obsolete, but kept there for the record.

As of 3DNA v2.1, the Ruby script "x3dna_ensemble" should be used for the analysis of NMR ensembles or MD simulation trajectories. Type -h for detailed info, and run the examples to get familiar with its usage/functionality.

Your attached PDB file contains only one model, so you can use the find_pair/analyze combination to calculate 3DNA parameters. Note, however, your structure has poor geometry, as shown in the image below. As a rule, one should always perform "sanity" check to ensure sensible results.

HTH,

Xiang-Jun

1317

General discussions (Q&As) / Re: Single Strand DNA (ssDNA) 3D structure prediction

« on: April 06, 2012, 07:52:19 am »

No, I'm not saying or intending to imply that ssDNA and ssRNA are energetically equivalent. However, from a practical prospective, first it'd be better to have something than nothing. Second, a prediction is just a prediction, it is no guarantee that the "predicted" structure is "real" or even "meaningful": just think about how many predictions you can have from the same program with different settings, not to mention the different software tools available. Third, the recent article "RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction" [April 2012 [18 (4)] issue of the RNA journal] serves as a proof of my point. In theory (and in practice), a software can easily "predict" many more protein/DNA/RNA structures than the PDB has accumulated over the past 40 years.

Aside from all the augments above, 3DNA does not deal with "energetics" at all (in its current version, at least) -- it is purely geometrical.

Xiang-Jun

1318

MD simulations / Re: How to properly use x3dna_ensemble?

« on: April 05, 2012, 01:29:28 pm »

BUT, when I do "x3dna_ensamble analyze" for multiple snapshots, I do not see helical axis vectors in the output file.

The information you need, "Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step",  is not parsed in the current version of x3dna_ensemble. I will get it added soon and keep you updated.

Xiang-Jun
 

1319

General discussions (Q&As) / Re: Single Strand DNA (ssDNA) 3D structure prediction

« on: April 05, 2012, 07:32:33 am »

See the thread "changing secondary structure to tertiary structure of ssDNA".

For RNA we have some software such as Rosetta to predict 3D structure

Does it make sense to start from the same secondary structure you have, but simply change Ts to Us, and predict a 3D RNA structure using Rosetta etc. Then you can delete O2' atoms, and mutate Us to Ts with mutate_bases that will preserve backbone conformation and base-pairing geometry.

Xiang-Jun

1320

w3DNA -- web interface to 3DNA / Re: changing secondary structure to tertiary structure of ssDNA

« on: April 04, 2012, 07:36:52 am »

See my previous reply. In short, 3DNA is not directly up to your purpose yet, even though some of its components may be useful in certain part of your workflow. The recent "RNA-Puzzles" paper in the RNA journal is the state-of-the-art on predicting DNA/RNA tertiary structures.

Good luck with your project.

Xiang-Jun

1321

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 04, 2012, 07:29:15 am »

Hi Vandana,

I am a bit surprised that you cannot run the basic 'pwd' (present working directory) command in you MinGW/MSYS -- Windows 7 system. Anyway, I'm glad to know that you've got 3DNA up and running; now you can start to play around with 3DNA. If you have any questions, do not heistate to post back on the forum!

Xiang-Jun

1322

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 03, 2012, 01:45:28 pm »

Hi Vandana,

Sorry to hear your problem in setting up 3DNA on Windows 7 using MinGW/MSYS. To help identify where the problem is, please do the followings:

• First, change into the 3DNA bin/ directory
• Then type: pwd, what is the output?
• What's the output of ruby -v?
• If the above step runs successfully, what's the output of ruby x3dna_setup?

Xiang-Jun

1323

General discussions (Q&As) / Re: A-DNA definition

« on: April 02, 2012, 03:12:55 pm »

Hi Arnab,

However, what I really meant is to supply the coordinate directly from xtc to 3DNA directly bypassing the pdb so that the analysis is extremely fast.

I see your point. By adhering to the standard MODEL/ENDMDL delineated PDB format, however, x3dna_ensemble can handle directly an NMR ensemble. Via a purpose-specific format adaptor, the script should be applicable to the analysis of simulation trajectories from any third-party MD package. Intuitively, I feel this approach is simple, flexible, and practical. Of course, only 3DNA users, especially MD practitioners, can judge if x3dna_ensemble is able to meet real-world challenges. Please share your experience.

Xiang-Jun
 

1324

General discussions (Q&As) / Re: A-DNA definition

« on: April 02, 2012, 11:43:41 am »

Hi Arnab,

I'm glad our conversation in this thread helped clear your doubt. It has been at least several years since I looked at the details about the classification of dinucleotide steps in 3DNA. Your questiones refreshed my memory on this topic.

From the output files you attached, I know you are using 3DNA v2.0. Did you know that as of v2.1, 3DNA provides a Ruby script x3dna_ensemble for the analysis of MD simulation trajectories? The help info is as below:

Code: [Select]

x3dna_ensemble -h
------------------------------------------------------------------------
Utilities for the analysis and visualization of an ensemble
    Usage: x3dna_ensemble [-h|-v] sub-command [-h] [options]
    where sub-command must be one of:
        analyze -- analyze MODEL/ENDMDL delineated ensemble (NMR or MD)
        block_image -- generate a base block schematic image
        extract -- extract structural parameters after running 'analyze'
        reorient -- reorient models to a particular frame/orientation
------------------------------------------------------------------------
  --version, -v:   Print version and exit
     --help, -h:   Show this message

Note that the script starts with a MODEL/ENDMDL delineated ensemble or a collection of individual entries in the standard PDB format. For an example, see the directory $X3DNA/examples/ensemble/md, and run the following to see the possibilities:

Code: [Select]

x3dna_ensemble analyze -h
x3dna_ensemble extract -h

If you don't have time and need additional pair of hands, I can create a patch between GROMACS and 3DNA where a GROMACS trajectory can be analyzed for all 3DNA related information.

To make 3DNA better sever the community, I really need help from responsive and enthusiastic 3DNA users like you! The script x3dna_ensemble currently does not directly read a third-party specific trajectory file, so I have been planning to add a convert sub-command with options for GROMACS, Amber, CHARMM etc. Your contribution to "create a patch between GROMACS and 3DNA where a GROMACS trajectory can be analyzed for all 3DNA related information" is certainly welcome.

To consolidate our efforts, could you please do the following:

• Download and install 3DNA v2.1beta, and try out the examples mentioned above to see how the new facilities help your workflow.
• Check to see how much can be provided from GROMACS. In a recent thread titled "How to properly use x3dna_ensemble?", I become aware of the fact that "Gromacs can actually devide an xtc-trajectory file into separate pdb files in MODEL/ENDML format."
• After checking the above two points, we can focus on what are still missing or inconvenient.

Best regards,

Xiang-Jun

1325

General discussions (Q&As) / Re: A-DNA definition

« on: April 01, 2012, 05:24:57 pm »

Hi Arnab,

Thanks for your follow up. I am impressed by your attention to the little "details" -- oftentimes, the small part counts a lot.

Therefore, I assume there must be more to the story.

You are absolutely right -- see below for details.

To add to my previous post,  the sanity check clears out str221.pdb for 6CG/CG step which has Zp 1.93 but unassigned type. However, I don't know the check corresponding to "WC_info && WC_info[i + 1]  /* WC geometry */". Therefore, this may be a part of the issue of not getting the right form.

From the two PDB files you attached, it is easy to verify that all bps are of standard Watson-Crick type. So there is no issue with sanity check on WC_info(i) and WC_info(i + 1).

The real underlying reason for your observed discrepancy between str221 and str226 is as follows: to be on the safe side, 3DNA performs an additional check before assigning a dinucleotide step into A-, B- or TA-DNA form: there must be at least two consecutive dinucleotide steps of the same type to avoid any single isolated (mostly spurious) "transition" step.

Take your str221.pdb as an example,

    step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 GC/GC   -4.05    9.12   -1.51   -1.02    8.24   -4.15
   2 CG/CG   -2.24    8.83    0.29   -1.71    8.83    0.32     B
   3 GC/GC   -4.06    9.10   -0.65   -6.93    8.67    2.77     B
   4 CA/TG   -3.22    9.18    0.30   -7.45    8.28    4.02
   5 AC/GT   -3.17    9.21    1.03   -5.69    9.14    1.49
   6 CG/CG   -3.38    8.33    1.93   -7.49    8.45    1.33
   7 GT/AC   -3.58    8.97    0.80   -7.40    8.81    1.83
   8 TG/CA   -4.26    8.76   -0.67   -9.08    6.51    5.89
   9 GC/GC   -2.30    8.70   -0.08   -0.73    8.70    0.21     B
  10 CG/CG   -3.74    9.22   -0.75   -7.66    8.74    2.97     B
  11 GC/GC   -2.90    9.03    0.30   -5.61    8.55    2.92     B

According to the criteria detailed in my previous reply, step 6 CG/CG is indeed classified as A-DNA, since its Zp (1.93) > 1.5 Å. However, each of its neighbors -- 5 AC/GT and 7 GT/AC -- has a Zp < 1.5 Å, so neither is in A-form. Thus, 6 CG/CG is downgraded as unclassified. Note that without this additional check, step 4 CA/TG would have been taken as TA-DNA [Zp(h) = 4.02 > 4.0 Å].

With the above note, one can see easily why step 6 CG/CG in str226 is classified as A-DNA -- it's simply because its neighbor 5 AC/GT is also A-DNA.

    step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 GC/GC   -4.37    8.77   -1.05   -4.95    8.83   -0.22     B
   2 CG/CG   -2.56    8.63    0.13   -2.38    8.49    1.55     B
   3 GC/GC   -3.74    9.12   -0.62   -4.46    9.06   -1.34     B
   4 CA/TG   -2.64    9.32    0.91   -6.75    7.91    5.00
   5 AC/GT   -3.16    9.32    1.56   -7.39    9.41    0.91     A
   6 CG/CG   -3.07    8.71    2.09   -7.45    8.73    1.93     A
   7 GT/AC   -3.49    9.02    0.43   -6.64    8.97    1.09     B
   8 TG/CA   -3.83    9.27   -0.68   -7.64    9.09    1.94     B
   9 GC/GC   -2.69    8.96    0.34   -2.36    8.95    0.55     B
  10 CG/CG   -4.15    8.96   -0.57   -7.70    8.62    2.56     B
  11 GC/GC   -3.43    8.71    1.58   -6.69    8.70    1.66

I may refine the criteria used for dinucleotide classification in future release of 3DNA, and I welcome your feedback. For your analysis of MD simulation trajectories, I'd suggest that you check directly the raw data (Xp, Yp, Zp, XpH, YpH, ZpH etc).

HTH,

Xiang-Jun