Messages

1201

General discussions (Q&As) / Re: different geometries

« on: November 06, 2012, 10:18:50 am »

Could you be more specific by providing an example to put your question in context?

Xiang-Jun

1202

General discussions (Q&As) / Re: DNA elastic parameters from NDB database

« on: November 05, 2012, 11:32:27 am »

No, these new values are not included in 3DNA. You're advised to contact the authors of the 2009 Balasubramanian paper for further details.

For those who are interested in the original Olson et al. 1998 dataset, please check the post "Some details on PNAS98 DNA sequence-dependent deformability".

Xiang-Jun

1203

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

« on: November 03, 2012, 12:28:40 pm »

Hi Ludo,

Thanks for reporting the w3DNA server problem. It is indeed down right now, possibly due to Hurricane Sandy. I've informed those in change at Rutgers, and hopefully w3DNA will be back soon.

Xiang-Jun

1204

General discussions (Q&As) / Re: different geometries

« on: October 29, 2012, 04:12:43 pm »

It's closer, but still not a proper PDB format -- see the thread "how the cartesian coordinates transform to PDB format" for details.

Given the fact that this issue has popped up quite a few times over the years, I may consider adding support in 3DNA to make such conversion more straightforward.

Xiang-Jun

1205

General discussions (Q&As) / Re: different geometries

« on: October 29, 2012, 01:06:52 pm »

Thanks for posting back an example molden file which help clarify the issue. No, that's not the format recognized by 3DNA programs. Currently, 3DNA only accepts PDB format file (coordinate record descriptions) as documented in the RCSB website. That said, it's feasible to convert your molden file via a purpose-oriented script or third-party utility -- Google search may help.

Xiang-Jun

1206

Bug reports / Re: open_file <./Atomic.g.pdb> failed: No such file or directory

« on: October 26, 2012, 01:46:07 pm »

As a follow up, as of 3DNA v2.1 2012oct26, your initial problem has been solved. Now you can have for example only Atomic_A.pdb in your current working directory, and 3DNA will use that file; for the Atomic*.pdb files not found in the current directory, 3DNA will use the default in $X3DNA/config. Overall, this revision allows 3DNA users greater flexibility in choosing the standard base-reference-frame files for analysis and rebuilding.

Xiang-Jun

1207

General discussions (Q&As) / Re: different geometries

« on: October 26, 2012, 01:37:31 pm »

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

Could you be more specific by providing a concreate example to show us what a molden file look like?

Xiang-Jun

1208

FAQs / How can I mutate cytosine to 5-methylcytosine

« on: October 26, 2012, 01:23:14 pm »

Methylation of cytosines in DNA is a crucial epigenetic modification that regulate expression of many genes. Chemically, it is the addition of a methyl group to the 5 position of cytosine (C).

The mutate_bases program in 3DNA v2.x performs in silico base mutations given a nucleic acid structure in PDB format. It is not a problem to mutate any C to a 5-methylcytosine (5CM) provided that users set a 5CM in its standard base reference frame. Given the importance of 5CM in epigenetics and the increasing simulation studies to understand its effects, I have included Atomic_5CM.pdb in the 3DNA v2.1 distribution as of 2012oct26.

According to PDB, the three-letter nucleotide name for 5-methylcytosine is 5CM instead of 5MC -- see for example PDB entries 4mht and 2uz4. The methyl carbon is named " C5A" instead of " C5M" or " C7 ". Thus, the content of the Atomic_5CM.pdb file is:

Code: [Select]

REMARK    3DNA by Dr. Xiang-Jun Lu [2012-10-26] (xiangjun@x3dna.org)
ATOM      1  C1' 5CM A   1      -2.477   5.402   0.000  1.00  0.00           C 
ATOM      2  N1  5CM A   1      -1.285   4.542   0.000  1.00  0.00           N 
ATOM      3  C2  5CM A   1      -1.472   3.158   0.000  1.00  0.00           C 
ATOM      4  O2  5CM A   1      -2.628   2.709   0.001  1.00  0.00           O 
ATOM      5  N3  5CM A   1      -0.391   2.344   0.000  1.00  0.00           N 
ATOM      6  C4  5CM A   1       0.837   2.868   0.000  1.00  0.00           C 
ATOM      7  N4  5CM A   1       1.875   2.027   0.001  1.00  0.00           N 
ATOM      8  C5  5CM A   1       1.056   4.275   0.000  1.00  0.00           C 
ATOM      9  C5A 5CM A   1       2.466   4.961   0.001  1.00  0.00           C 
ATOM     10  C6  5CM A   1      -0.023   5.068   0.000  1.00  0.00           C 
END
With this new addition, it is now very straightforward to mutate Cs to 5CMs with mutate_bases, as illustrated by the following two examples:

• Mutate C1 on chain A and C23 on chain B of the Dickerson B-DNA dodecamer (PDB entry 355d) to 5CMs:
  

  mutate_bases 'chain=A snum=1 m=5CM; chain=B snum=23 m=5CM' 355d.pdb 355d_AC1BC23_5CM.pdb

• Mutate C2 on chain A of the yeast phenylalanine tRNA (PDB entry 6tna) to 5CM:
  

  mutate_bases 'chain=A snum=2 name=C m=5CM' 6tna.pdb 6tna_C2_5CM.pdb

The mutated files 355d_AC1BC23_5CM.pdb and 6tna_C2_5CM.pdb are attached for your verification. For comparison, shown below are the original atomic coordinates of the above tRNA 6tna cytosine and coordinates of its 5CM mutant in red. Note that the coordinates of the backbone atoms are the same, and coordinates of common base atoms are very close.

• The original atomic coordinates of a cytosine from PDB entry 6tna:
  --------------------------------------------------------------------------------
  ATOM     25  P     C A   2      31.659  20.469  70.978  1.00 10.00           P  
  ATOM     26  OP1   C A   2      32.973  21.044  71.364  1.00 10.00           O  
  ATOM     27  OP2   C A   2      30.973  21.143  69.849  1.00 10.00           O  
  ATOM     28  O5'   C A   2      31.815  18.912  70.652  1.00 10.00           O  
  ATOM     29  C5'   C A   2      30.629  18.184  70.293  1.00 10.00           C  
  ATOM     30  C4'   C A   2      30.507  16.914  71.139  1.00 10.00           C  
  ATOM     31  O4'   C A   2      29.293  17.051  71.947  1.00 10.00           O  
  ATOM     32  C3'   C A   2      30.455  15.607  70.367  1.00 10.00           C  
  ATOM     33  O3'   C A   2      31.724  14.971  70.316  1.00 10.00           O  
  ATOM     34  C2'   C A   2      29.411  14.815  71.146  1.00 10.00           C  
  ATOM     35  O2'   C A   2      29.987  14.227  72.301  1.00 10.00           O  
  ATOM     36  C1'   C A   2      28.473  15.927  71.630  1.00 10.00           C  
  ATOM     37  N1    C A   2      27.474  16.346  70.621  1.00 10.00           N  
  ATOM     38  C2    C A   2      26.658  15.368  70.068  1.00 10.00           C  
  ATOM     39  O2    C A   2      26.802  14.198  70.441  1.00 10.00           O  
  ATOM     40  N3    C A   2      25.726  15.730  69.143  1.00 10.00           N  
  ATOM     41  C4    C A   2      25.601  17.008  68.767  1.00 10.00           C  
  ATOM     42  N4    C A   2      24.682  17.314  67.872  1.00 10.00           N  
  ATOM     43  C5    C A   2      26.436  18.041  69.324  1.00 10.00           C  
  ATOM     44  C6    C A   2      27.351  17.658  70.243  1.00 10.00           C  
  --------------------------------------------------------------------------------
  The coordinates of the mutant 5-methylcytosine generated by 'mutate_bases'
  REMARK    Mutation#1 A:...2@:[..C] to [5CM]
  ATOM     25  P   5CM A   2      31.659  20.469  70.978  1.00 10.00           P  
  ATOM     26  OP1 5CM A   2      32.973  21.044  71.364  1.00 10.00           O  
  ATOM     27  OP2 5CM A   2      30.973  21.143  69.849  1.00 10.00           O  
  ATOM     28  O5' 5CM A   2      31.815  18.912  70.652  1.00 10.00           O  
  ATOM     29  C5' 5CM A   2      30.629  18.184  70.293  1.00 10.00           C  
  ATOM     30  C4' 5CM A   2      30.507  16.914  71.139  1.00 10.00           C  
  ATOM     31  O4' 5CM A   2      29.293  17.051  71.947  1.00 10.00           O  
  ATOM     32  C3' 5CM A   2      30.455  15.607  70.367  1.00 10.00           C  
  ATOM     33  O3' 5CM A   2      31.724  14.971  70.316  1.00 10.00           O  
  ATOM     34  C2' 5CM A   2      29.411  14.815  71.146  1.00 10.00           C  
  ATOM     35  O2' 5CM A   2      29.987  14.227  72.301  1.00 10.00           O  
  ATOM     36  C1' 5CM A   2      28.473  15.927  71.630  1.00 10.00           C  
  ATOM     37  N1  5CM A   2      27.475  16.353  70.620  1.00  1.00           N  
  ATOM     38  C2  5CM A   2      26.651  15.372  70.062  1.00  1.00           C  
  ATOM     39  O2  5CM A   2      26.789  14.195  70.427  1.00  1.00           O  
  ATOM     40  N3  5CM A   2      25.726  15.730  69.141  1.00  1.00           N  
  ATOM     41  C4  5CM A   2      25.610  17.009  68.776  1.00  1.00           C  
  ATOM     42  N4  5CM A   2      24.685  17.316  67.863  1.00  1.00           N  
  ATOM     43  C5  5CM A   2      26.437  18.028  69.328  1.00  1.00           C  
  ATOM     44  C5A 5CM A   2      26.359  19.547  68.947  1.00  1.00           C  
  ATOM     45  C6  5CM A   2      27.347  17.660  70.238  1.00  1.00           C  

1209

Bug reports / Re: open_file <./Atomic.g.pdb> failed: No such file or directory

« on: October 24, 2012, 11:11:33 am »

Hi Mauricio,

Thanks for your report. I can reproduce the 'problem'; it has nothing to do with including $X3DNA/config in the environment settings.

The error message:

Code: [Select]

open_file <./Atomic.g.pdb> failed: No such file or directorymeans 3DNA (find_pair) is trying to locate the file in your current working directory (CWD), instead of the default system setting $X3DNA/config where the file Atomic.g.pdb is available, among other Atomic*.pdb files.

If file Atomic_A.pdb exists in your CWD, 3DNA assumes all other Atomic*.pdb files there as well. That's normally true if you run, e.g.:

Code: [Select]

x3dna_utils cp_std bdna
For your case, you must have Atomic_A.pdb and possibly several other canonical base Atomic_[CGTU].pdb files in your CWD, but not the modified version (in lower case, prefixed with a dot instead of underscore). So simply run the following command in you CWD will do the trick:

Code: [Select]

cp -f $X3DNA/config/Atomic.*.pdb .
Alternatively, you can delete all the Atomic*pdb files from your CWD, and find_pair will work as expected:

Code: [Select]

rm -f Atomic*.pdb
find_pair 1ehz.pdb stdout
Please have a try and report back how it goes.

I may consider to refine 3DNA to check for each Atomic*.pdb file separately, but that would complicate the code. You are actually the first to notice this 'limitation'. Practically, knowing what's happening behind the scene, you can easily work around it, as suggested above.

HTH,

Xiang-Jun

1210

General discussions (Q&As) / Re: Question on base-step parameters calculation in 3DNA

« on: October 19, 2012, 12:02:56 am »

Thanks for reading the "technical details" -- you are one of the very few users I am aware of who actually work through the examples.

Regarding your specific question, you are right in noticing that the x- and y-axes (the first two columns) of Rm are not the raw average of the corresponding columns of R1' and R2':

(-0.6616 -0.1982)/2 =-0.4299, which was different to the given value -0.4490

Here Rm, as a proper rotation matrix, is orthonormal; its x-axis and y-axis are normalized, which is precisely where the discrepancy comes from.

HTH,

Xiang-Jun
PS. In going through the doc, I've also noticed a typo in step #2 of section 5.5, where the RollTilt angle should be in degrees instead of Angstroms. I am planning to update the technical details and put it on the web. If you notice anything that can be improved, please post back.

1211

General discussions (Q&As) / Re: DNA structure with sequence-dependent structural characteristics

« on: October 14, 2012, 08:11:02 pm »

Hi Christos,

To clarify, 3DNA's rebuild program can generate an 'arbitrary' DNA (or RNA) structure based on a set of base-pair (optional) and step (or helical) parameters. It is a mechanic process since the program does not check or care if the structure is realistic or not. It is mathematically rigorous because you can 'analyze' the generated structure to get  exactly the parameters you start with.

Now to your question -- yes, it is possible to "create DNA structures with sequence-dependent characteristics". As a practical example, see recipe #2 "Determination of DNA curvature associated with different roll distributions" in the 2008 3DNA Nature Protocols paper. As for building DNA structures with "minor groove compression in PURINEpPYRIMIDINE steps, compression of major groove in PYRIMIDINEpPURINE steps", it is up to you to derive the "correct" base sequence and base-pair parameters to feed into rebuild.

HTH,

Xiang-Jun

1212

General discussions (Q&As) / Re: no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat

« on: October 06, 2012, 12:36:24 pm »

Well, you have not yet downloaded the 2012oct06 updated version I just compiled to solve the naming issue you experiences (see What's new?). The file should be named: x3dna-v2.1-linux-64bit-2012oct06.tar.gz.

Xiang-Jun

1213

General discussions (Q&As) / Re: no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat

« on: October 06, 2012, 10:42:57 am »

Okay, please download the 2012oct06 updated (beta) version of v2.1 and try again. The atom naming issues should have been resolved. Please report back whether reinstalling the revised version does help.

Xiang-Jun

1214

General discussions (Q&As) / Re: no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat

« on: October 05, 2012, 03:54:19 pm »

Hi Asmita,

Thanks for joining the 3DNA-user community!

Posting your question on the forum is a good first step; attaching a specific example so that your problem can be reproduced is better still.

The problem is due to the non-standard format of your PDB file, as shown below:

# The following is extracted from your attached "struct_1.pdb"
ATOM     30 P    G       2      -3.465  14.386  -4.840  0.00  0.00
ATOM     31 OP1  G       2      -4.272  15.372  -4.078  0.00  0.00
ATOM     32 OP2  G       2      -2.267  13.805  -4.173  0.00  0.00
ATOM     17  P    DG A   2      23.337  31.278  21.156  1.00 13.26           P  
ATOM     18  OP1  DG A   2      24.761  31.571  21.391  1.00 13.17           O  
ATOM     19  OP2  DG A   2      22.651  31.834  19.956  1.00 12.34           O
# The above in red is taken from PDB entry 355d  
 

As you can see clearly, the atom name (and residue name) in your PDB file is shifted to the left by one column. So the atom name for OP1 is taken as

"OP1 " instead of the normal " OP1", 

and that explains the message you saw:

no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat'

Adding an entry "OP..   O" (note the two dots in place of digit and space) to file 'atomlist.dat' will make the info message go away.

The most effective way to fix such problems is to ensure your PDB file is standard compliant [see Coordinate File Description (PDB Format)]. In your case, ask the developers of your MD package to generate standard compliant PDB file, or you can write a simple script to make the changes. This is the first time I am aware of such problem; given enough interest, I will consider to refine 3DNA to accommodate such non-standard cases.

HTH,

Xiang-Jun

1215

MD simulations / Re: Using find_pair

« on: September 18, 2012, 11:33:25 pm »

Hi Johnny,

Thanks for your follow-up; it certainly helps clarify the situation:

The output of "uname -a" means your Ubuntu is 32-bit -- google "ubuntu 32 bit or 64 bit how to tell" for details. This explains why the 3DNA 64-bits version "was not compatible" on your machine.

So if you insist on using Ubuntu instead of Mac OS X, a Ubuntu 64-bit version seems the way to go.

Xiang-Jun

1216

General discussions (Q&As) / Data files for Table 3 of the standard base-reference frame article

« on: September 18, 2012, 10:32:15 pm »

Table 3 of the Olson et al. (2001) "standard base-reference frame article" lists the mean values and standard deviations of base geometric parameters for high resolution A-DNA and B-DNA crystal structures, as shown below.

The selection criteria of the A- and B-DNA datasets have recently been reported in the thread "Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper". For the sake for easy reference and completeness, here is the note again:

Selection Criteria:
   NDB ID: ad OR bd
   Classification: DNA
   Structure Description: Double Helix
   Conformation Type: A OR B
   No Drug, No Mismatch
   No Modifiers (Base/Sugar/Phosphate)
   Resolution better than 2.0 A
   =======================
   34 A-DNA and 27 B-DNA

For B-DNA, delete bd0012, bd0013 & bdf068 (following HMB)
   bd0001 bd0006_A
   bd0014: coordinates from PDB 463D
   bd0005 bd0016_A (with repeated atoms!)
   bd0018 bd0019 bdj017 bdj019 bdj025 bdj031 bdj036 bdj037 bdj051
   bdj052 bdj060 bdj061 
   bdj081 (Uses helix #1 with strands A and B. The other two are
           disordered)
   bdl001 bdl005 bdl020 bdl084
   bd0023_A  bd0029
   -------------------------- 27-3=24 structures

For A-DNA
   ad0002 ==> (ad0002_AB + ad0002_CD)
   ad0003 ad0004 adh008 adh010 adh0102 adh0103 adh0104 adh0105
   adh014 adh026 adh027 adh029 adh033 adh034 adh038 adh039 adh047
   adh070 adh078 adj0102 adj0103 adj0112 adj0113 adj022 adj049
   adj050 adj051 adj065 adj066 adj067 adj075 
   adl025 (suspicious! big Buckle, alternating Propeller)
   adl047 (with B-steps, not good either!)
   -------------------------- 34+1-2=33 structures

Outliers:
  A-DNA: ad0002_CD, steps 3-4,   bps 3-4-5
         ad0004,    steps 3-4-5, bps 3-4-5-6
  B-DNA: bdj025,    step 3,      bps 3-4
         bdj031,    step 3,      bps 3-4
         bdj037,    step 3,      bps 3-4

The six data files themselves are attached below; here the A- prefix is for A-DNA, and B- prefix for B-DNA:

• 'A-base-pair.dat' and 'B-base-pair.dat' contain the base-pair parameters in the order of Shear, Stretch, Stagger, Buckle, Propeller, and Opening.
• 'A-step-pars.dat' and 'B-step-pars.dat' contain the step parameters in the order of Shift, Slide, Rse, Tilt, Roll and Twist.
• 'A-heli-pars.dat' and 'B-heli-pars.dat' contain the helical parameters in the order of x-displacement, y-displacement, Helical rise, Inclination, Tip, and Helical twist.

While the Table content is derived from NDB entries with only Watson-Crick base pairs in A- and B-DNA duplexes, it serves as a reference for identifying/quantifying non-canonical (mismatched) pairs by taking advantage the base-pair parameters. This approach is rigorous in its description of the relative base geometry in a pair, and is distinct from and complement with the Leontis-Westhof classification scheme.

1217

MD simulations / Re: Using find_pair

« on: September 18, 2012, 09:52:28 pm »

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

Which version of 3DNA are you using:, v1.5, v2.0 or v2.1beta? What's your Linux variant -- what's the output of running "uname -a"?

What do you mean specifically that you could run the huge 2GB+ pdb file easily on your Mac? Using "find_pair" or other programs?

This is the first time I meet such a question, so I have more questions to you before I could possibly provide a solution.

Xiang-Jun

1218

General discussions (Q&As) / Re: Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper

« on: September 07, 2012, 02:15:17 pm »

Thanks for your patience -- it took me quite some time to dig into my files used for the 2003 3DNA paper! Luckily, I got them, and the time has been well-worth spent .

Here are the details -- the whole datasets and scripts can be downloaded by following the link: 3DNA-NAR03-Fig5.tar.gz. Figure 5(a)-(c) generated with the scripts and data files are attached.

• Content of the README file:
  

  This folder (3DNA-NAR03-Fig5) contains all the data files and scripts
  to reproduce Figure 5 of the 2003 3DNA paper in Nucleic Acids Research
  (NAR03). The contents are taken from the original materials I used to
  create Figure 5 of NAR03, with slight editing. Specifically, I revised
  the Matlab scripts to work in GNU Octave v3.2.4 for verification.
  
  If you have any questions or comments, please do post them on the 3DNA
  Forum.
  
  2012-09-06 -- Xiang-Jun Lu (http://x3dna.org)
  
  ========================================================================
  
  Data selections:
      'note-AB-datasets' -- datasets of selected A- and B-DNA structures
      'note-TA-dataset'  -- dataset of selected TA-DNA structures
  
  Data files:
      'A-heli-pars.dat' -- six helical parameters 
      'A-step-pars.dat' -- six step parameters
      'A-zp-zph.dat'    -- Zp and ZpH parameters
          Selected parameters of the A-DNA dataset. Note that the order
          the parameters is as in .out file from running 'analyze'
  
      'B-heli-pars.dat',  'B-step-pars.dat',  'B-zp-zph.dat' for B-DNA
      'TA-heli-pars.dat', 'TA-step-pars.dat', 'TA-zp-zph.dat' for TA-DNA
  
  Scripts:
      'incl_xdsp.m' -- script to generate Figure 5(a), Inclination vs Tip
                    'incl_xdsp.png' -- output file from running the script
      'roll_slide.m' -- script to generate Figure 5(b), Roll vs Slide
                    'roll_slide.png' -- output file from running the script
      'zph_zp.m' -- script to generate Figure 5(c), Zp(h) vs Zp
                    'zph_zp.png' -- output file from running the script
      'draw_ellipse.m', 'get_pars.m', 'open_file.m' -- supporting scripts
  

• Content of file note-AB-datasets
  

  Selection Criteria:
     NDB ID: ad OR bd
     Classification: DNA
     Structure Description: Double Helix
     Conformation Type: A OR B
     No Drug, No Mismatch
     No Modifiers (Base/Sugar/Phosphate)
     Resolution better than 2.0 A
     =======================
     34 A-DNA and 27 B-DNA
  
  For B-DNA, delete bd0012, bd0013 & bdf068 (following HMB)
     bd0001 bd0006_A
     bd0014: coordinates from PDB 463D
     bd0005 bd0016_A (with repeated atoms!)
     bd0018 bd0019 bdj017 bdj019 bdj025 bdj031 bdj036 bdj037 bdj051
     bdj052 bdj060 bdj061 
     bdj081 (Uses helix #1 with strands A and B. The other two are
             disordered)
     bdl001 bdl005 bdl020 bdl084
     bd0023_A  bd0029
     -------------------------- 27-3=24 structures
  
  For A-DNA
     ad0002 ==> (ad0002_AB + ad0002_CD)
     ad0003 ad0004 adh008 adh010 adh0102 adh0103 adh0104 adh0105
     adh014 adh026 adh027 adh029 adh033 adh034 adh038 adh039 adh047
     adh070 adh078 adj0102 adj0103 adj0112 adj0113 adj022 adj049
     adj050 adj051 adj065 adj066 adj067 adj075 
     adl025 (suspicious! big Buckle, alternating Propeller)
     adl047 (with B-steps, not good either!)
     -------------------------- 34+1-2=33 structures
  
  Outliers:
    A-DNA: ad0002_CD, steps 3-4,   bps 3-4-5
           ad0004,    steps 3-4-5, bps 3-4-5-6
    B-DNA: bdj025,    step 3,      bps 3-4
           bdj031,    step 3,      bps 3-4
           bdj037,    step 3,      bps 3-4
  

• Content of file note-TA-dataset
  

  pd0070, pd0112, pd0154, pd0155, pd0156 pd0157, pd0158, pd0159, pd0160,
  pd0161, pd0162, pd0163, pd0164, pdr031 pdt009, pdt012, pdt024, pdt025,
  pdt032, pdt034, pdt036
  
  This directory contains TATA box segments. It is normally 8-bp long, and
  has the sequence: T-A-T-A-@-A-@-N. There are two kinks at the terminal
  steps.
  
  * means non-WC base-pair which is eliminated from further analysis
  
  NDB ID  ##     Sequence      Res(A)  R-fac(%) chainID and residue range
  --------------------------------------------------------------------
  pd0070  01  T-T-T-A-A-A-T-A   2.4     20.0   C 1410 1417 D 1432 1439
                             
  pd0112  02  T-A-T-A-A-A-A-G   2.65    23.1   K 8 15 L 105 112
          03  T-A-T-A-A-A-A-G                  C 8 15 D 105 112
          04  T-A-T-A-A-A-A-G                  G 8 15 H 105 112
          05  T-A-T-A-A-A-A-G                  O 8 15 P 105 112
          06  T-A-T-A-A-A-A-G                  S 8 15 T 105 112
                                        
  pd0154  07  T-A-T-A-A-A-A-T   1.86    21.0   C 203 210 D 219 226
          08  T-A-T-A-A-A-A-T                  E 203 210 F 219 226
                                     
  pd0155  09  T-A-T-A-A-G-A-G*  1.93    19.6   C 203 209 D 220 226
          10  T-A-T-A-A-G-A-G*                 E 203 209 F 220 226
     
  pd0156  11  T-A-T-A-A-T-A-G*  2.1     19.3   C 203 209 D 220 226
          12  T-A-T-A-A-T-A-G*                 E 203 209 F 220 226
                                     
  pd0157  13  T-A-T-A-T-A-A-G*  2.3     19.4   C 203 209 D 220 226
          14  T-A-T-A-T-A-A-G*                 E 203 209 F 220 226
                                     
  pd0158  15  T-A-T-T-A-A-A-G*  2.1     19.4   C 203 209 D 220 226
          16  T-A-T-T-A-A-A-G*                 E 203 209 F 220 226
                                     
  pd0159  17  T-A-C-A-A-A-A-G*  1.9     20.9   C 203 209 D 220 226
          18  T-A-C-A-A-A-A-G*                 E 203 209 F 220 226
     
  pd0160  19  T-T-T-A-A-A-A-G*  1.8     19.3   C 203 209 D 220 226
          20  T-T-T-A-A-A-A-G*                 E 203 209 F 220 226
                                        
  pd0161  21  T-A-T-A-A-A-T-G*  2.23    19.1   C 203 209 D 220 226
          22  T-A-T-A-A-A-T-G*                 E 203 209 F 220 226
                                        
  pd0162  23  A-A-T-A-A-A-A-G*  2.3     18.2   C 203 209 D 220 226
          24  A-A-T-A-A-A-A-G*                 E 203 209 F 220 226
                                        
  pd0163  25  T-A-T-A-A-A-A-G   1.9     19.7   C 203 210 D 219 226
          26  T-A-T-A-A-A-A-G                  E 203 210 F 219 226
                                        
  pd0164  27  T-A-T-A-A-A-C*G*  1.95    19.9   C 203 208 D 221 226
          28  T-A-T-A-A-A-C*G*                 E 203 208 F 221 226
                                        
  pdr031  29  T-T-T-t-t-A-A-A   2.1     21.2   C 1408 1415 E 1420 1427
                                        
  pdt009  30  T-A-T-A-A-A-A-G   2.25    20.2   A 203 210 B 305 312
          31  T-A-T-A-A-A-A-G                  C 403 410 D 505 512
                                        
  pdt012  32  T-A-T-A-T-A-A-A   1.8     20.1   C 2 9 C 21 28
          33  T-A-T-A-T-A-A-A                  D 2 9 D 21 28
                                        
  pdt024  34  T-A-T-A-T-A-T-A   2.9     21.4   B 103 110 C 115 122
                                        
  pdt025  35  T-A-T-A-A-A-A-G   1.9     19.4   C 203 210 D 219 226
          36  T-A-T-A-A-A-A-G                  E 303 310 F 319 326
                                        
  pdt032  37  T-A-T-A-A-A-A-G   2.7     21.5   C 4 11 D 106 113
                                        
  pdt034  38  T-A-T-A-A-A-A-G   1.9     18.9   B 5 12 C 105 112
                                        
  pdt036  39  T-A-T-A-A-A-A-C   2.5     23.5   E 9 16 F 1 8
  

HTH,

Xiang-Jun

PS. As a matter of fact, the A- and B-DNA datasets are those used in Table 3 of the report on standard base reference.

1219

MD simulations / Re: About output files from x3dna_md.rb

« on: September 07, 2012, 12:31:11 pm »

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

Regarding your two questions:

1º) The missing atom messages are normal; they are for information only. "This structure has broken O3' to P[i+1] linkages" -- it means that there is an occurrence where nucleotides i and i+1 are not connected, as judged by out of range distance from O3'(i) to P(i+1). I am glad that you pay attention to this little detail. It may not be a concern -- you need to check a sample structure to be sure. If you need help, please attach such a structure with your follow up post.

2º) The two .out files are fine, and only 'RNA.out' is what you need. The example folder has four .out files correspond to the four different options:

Code: [Select]

  --ensemble, -e <s>:   Ensemble delineated with MODEL/ENDMDL pairs
    --models, -m <s>:   File containing an explicit list of model numbers
   --pattern, -p <s>:   Pattern of model files to process (e.g., *.pdb)
      --list, -l <s>:   File containing an explicit list of models
I am glad to see details on how 3DNA ('x3dna_md.rb' script) is being used.

I work in Gromacs program with Amber force field. I converted my trajectory, in separeted pdbs files such as example folder.

As noted above, the script can be run in four different modes, so you don't need to convert your trajectory into separate PDB files; the snapshots can be put into a single MODEL/ENDMDL delineated ensemble, as NMR structures in the PDB.

Note that in the current v2.1(beta), x3dna_md.rb has been replaced by x3dna_ensemble which has far more enhanced functionality. Please consider to update to the latest version.

HTH,

Xiang-Jun

1220

General discussions (Q&As) / Re: Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper

« on: August 31, 2012, 05:38:14 pm »

I'd like to ask about the DNA set used for the analysis that is presented in Fig 5. in the NAR 2003 paper. Are those structures previously classified as A, B and TA DNA by other means (?) before doing the Zp and Zp(h) calculations to confirm their differences? Where can I look for the structures which were used? (I guess it is somewhere in reference 81, Patikoglou,G.A. et al (1999))

Thanks for asking about the DNA datasets used in Figure 5 of the 3DNA 2003 NAR paper. Yes, the structures are previously assigned as A-, B- and TA-DNA by other means before we introduced Zp and Zp(h) to classify the three types of dinucleotide steps automatically. A- and B-DNA are based on conventional parameters (Slide/Roll, sugar puckers etc), as in the NDB, and the TA-DNA is mainly inspired by the work of Guzikevich‐Guerstein and Shakked (ref. 80):

A detailed structural analysis of two early examples of the TATA‐box DNA bound to the TATA‐box binding protein (TBP) (10,79) led Guzikevich‐Guerstein and Shakked (80) to propose that the 8 bp TATA‐box adopts a novel TA‐DNA conformation, different from either A or B DNA. The structures of many more such complexes have since been determined (81) and, as shown in Table 2 and Figure 5, all TATA‐box regions share similar conformational features.

So the complete list was not taken directly from somewhere in ref. 81, but compiled specifically for the work. The actual structure list used in producing Figure 5 for the TA-DNA steps can be found in the thread "DNA standards/statistics using 3DNA", dated August 2006. For A-DNA and B-DNA structures used in Figure 5 of the 2003 paper, I need to locate my original record from (nearly) a decade ago -- I will write a post about my findings on the 3DNA homepage, possibly by next week.

HTH,

Xiang-Jun

1221

General discussions (Q&As) / How to identify triplets, quadruplets and higher-order base associations

« on: August 16, 2012, 11:48:16 pm »

The find_pair -p option can find all base pairs and higher-order base associations. I implemented this option early on in 3DNA v1.x; yet in the 2003 Nucleic Acids Research paper and the corresponding find_pair -h output for v1.5, I deliberately omitted mentioning this functionality. I was hoping to further refine the algorithm/implementation, and to write up a detailed method paper on find_pair, a core 3DNA component. After leaving Rutgers nearly a decade ago, I've continuously maintained and refined 3DNA. However, for various reasons, up to now I've not been able to finish the long overdue 'technical' manuscript.

Over the years, numerous RNA structural bioinformatics resources have taken advantage of the functionality provided by find_pair; RNAView & BPS, two Rugters-based tools, are based directly on early versions of the program. It was only in the 3DNA 2008 Nature Protocols paper that I first illustrated the functionality of the find_pair -p option, in the protocol "identification of higher-order base associations in ribosomal RNA". This post provides further detailed examples so 3DNA users can take better advantage of this still underused functionality, useful in RNA structure related applications.

Let's create a new directory (folder), named 'find_pair-p-examples', and change to that directory. Now the directory is empty (check with ls).

Code: [Select]

mkdir find_pair-p-examples
cd find_pair-p-examples
ls
As an example, here we use the crystal structure of an RNA tetraplex (UGAGGU)₄ with A-tetrads, G-tetrads, U-tetrads and G-U octads: NDB id: ur0023; PDB id: 1j6s (see figure below). The structure was solved by Sundaralingam et al. at 1.4 Ångstroms resolution [Structure. 2003 Jul; 11(7):815-23]. Its asymmetric unit contains 4 single chains.The NDB/PDB provides 4 biological assemblies, each consisting of 4 identical chains from the asymmetric unit. Download biological assembly 1 from the NDB (or the PDB, if you prefer; but notice the case difference in PDB id):

Code: [Select]

wget ftp://ndbserver.rutgers.edu/NDB/coordinates/na-biol/1j6s.pdb1
Run find_pair -p on '1j6s.pdb1'. Note the -all_model option; by default, 3DNA programs (such as find_pair) handle only the first model (structure) in a given PDB data file.

Code: [Select]

find_pair -p -all_model 1j6s.pdb1 1j6s.mbp
At the end of output file '1j6s.mbp', one can see the following identified multiplets: one octad and three tetrads:

Code: [Select]

    1: #8 [1]...1>A:...1_:[BRU]u + [2]...1>A:...2_:[..G]G + [47]...2>A:...1_:[BRU]u + [48]...2>A:...2_:[..G]G + [93]...3>A:...1_:[BRU]u + [94]...3>A:...2_:[..G]G + [139]...4>A:...1_:[BRU]u + [140]...4>A:...2_:[..G]G
    2: #4 [3]...1>A:...3_:[..A]A + [49]...2>A:...3_:[..A]A + [95]...3>A:...3_:[..A]A + [141]...4>A:...3_:[..A]A
    3: #4 [4]...1>A:...4_:[..G]G + [50]...2>A:...4_:[..G]G + [96]...3>A:...4_:[..G]G + [142]...4>A:...4_:[..G]G
    4: #4 [5]...1>A:...5_:[..G]G + [51]...2>A:...5_:[..G]G + [97]...3>A:...5_:[..G]G + [143]...4>A:...5_:[..G]G
Among other outputs, there is also a file named 'multiplets.pdb' which contains the atomic coordinates of the corresponding multiplets, each oriented in its most-extended view. The base multiplets can be extracted with ex_str and then converted to .r3d format for Raster3D or PyMol rendering (see also post "What can 3DNA do for RNA structures?" for more examples).

Code: [Select]

ex_str -1 multiplets.pdb oct.pdb
r3d_atom -od -r=0.1 -b=0.2 oct.pdb stdout | render -png > oct.png

ex_str -2 multiplets.pdb A-tetrad.pdb
r3d_atom -od -r=0.1 -b=0.2 A-tetrad.pdb stdout | render -png > A-tetrad.png

ex_str -3 multiplets.pdb G-tetrad.pdb
r3d_atom -od -r=0.1 -b=0.2 G-tetrad.pdb stdout | render -png > G-tetrad.png

The three png images ('oct.png', 'A-tetrad.png' and 'G-tetrad.png') as generated directly above are attached below.

1222

Feature requests / Re: chain continuation character in analyze

« on: August 09, 2012, 07:43:01 am »

Hi Pascal,

I've implemented the -chain_markers option to analyze as of 3DNA v2.1beta dated 2012aug09. As an example, run the following commands,

Code: [Select]

find_pair -s 1egk.pdb stdout | analyze -chain_markers='+|x*' stdin
You will see the the portion below in output file '1egk.outs':

   1   (0.013) ....>A:...1_:[..A]A     +    
   2   (0.020) ....>A:...2_:[..G]G     |    
   3   (0.019) ....>A:...3_:[..G]G     |    
   4   (0.014) ....>A:...4_:[..A]A     |    
   5   (0.014) ....>A:...5_:[..G]G     |    
   6   (0.016) ....>A:...6_:[..A]A     |    
   7   (0.020) ....>A:...7_:[..G]G     |    
   8   (0.015) ....>A:...8_:[..A]A     |    
   9   (0.028) ....>A:...9_:[..G]G     |    
  10   (0.015) ....>A:..10_:[..A]A     |    
  11   (0.015) ....>A:..11_:[..U]U     |
  12   (0.022) ....>A:..12_:[..G]G     |
  13   (0.015) ....>A:..13_:[..G]G     |
  14   (0.021) ....>A:..14_:[..G]G     |
  15   (0.025) ....>A:..15_:[..U]U     |
  16   (0.016) ....>A:..16_:[..G]G     |
  17   (0.016) ....>A:..17_:[..C]C     |
  18   (0.016) ....>A:..18_:[..G]G     |
  19   (0.012) ....>A:..19_:[..A]A     |
  20   (0.017) ....>A:..20_:[..G]G     x
  21   (0.010) ....>B:..21_:[..C]C     +
  22   (0.018) ....>B:..22_:[..T]T     |
  23   (0.007) ....>B:..23_:[..C]C     |
  24   (0.016) ....>B:..24_:[..G]G     |
  25   (0.011) ....>B:..25_:[..C]C     |
  26   (0.013) ....>B:..26_:[..A]A     |
  27   (0.011) ....>B:..27_:[..C]C     |
  28   (0.006) ....>B:..28_:[..C]C     |
  29   (0.010) ....>B:..29_:[..C]C     |

As always, check it out and report back if that fits the bill.

Xiang-Jun

1223

Feature requests / Re: chain continuation character in analyze

« on: August 08, 2012, 12:00:46 pm »

I will think about the issue, and try to find a consistent way to handle find_pair in default and with the -s option, and streamline the output style between find_pair and analyze. I will post back in this thread once it is done.

The -pdbv3 is globally set to TRUE, so it also applies to o1p_o2p.

HTH

Xiang-Jun

1224

Feature requests / Re: chain continuation character in analyze

« on: August 08, 2012, 09:38:32 am »

The -chain_markers option works only for duplexes (default for find_pair), not yet with the -s option for single-stranded (ss) structures. 3DNA analyze checks for O3'(i) to P(i+1) distance with a cut-off of 2.5 Å for chain breaks; only two characters are used: 'x' for a break, and '-' for a covalent bond. I am a bit hesitated to make the current settings more complicated; you are the first 3DNA user to notice such little detailed info at all. Do you a solid use case to convince me?

In current 3DNA v2.1beta, no need to set -pdbv3; it's the default.

Xiang-Jun

1225

Feature requests / Re: chain continuation character in analyze

« on: August 06, 2012, 01:04:12 pm »

Please download the updated aug06 release of 3DNA v2.1beta. Now you can specify helix begin/continuation/end and isolated bp characters through option -chain_markers. For example,

Code: [Select]

find_pair 1egk.pdb stdout
    #  default as before
find_pair -chain_markers='o|x+' 1egk.pdb stdout
    #  with helix beginning character assigned to 'o'
The same option can also be applied to 'analyze'.

Also, as noted previously, the same strand P...P and C1'...C1' distances are now output in two decimals.

Have a try and report back how it goes.

Xiang-Jun