Messages

1176

General discussions (Q&As) / Re: question on +/- signs of local bp parameters

« on: January 11, 2013, 03:57:13 pm »

Thanks for providing an example that helps to illustrate the 'asymmetry' of the A-T vs T-A Hoogsteen pair when put in a structural context. The difference in opening can be understood in the same way as shear in G-U vs U-G wobble pair. See the figure below where the A and T on one strand are aligned on their base reference frames; note the different orientations of T and A.

In 3DNA, the Hoogsteen pair is of the M+N type; thus if the bases are swapped to N+M, all bp parameters change signs.

Code: [Select]

    3 T+A      -0.52      3.62      0.46     -6.35     10.24    -67.69
    4 A+T       0.60     -3.57     -0.56      6.51    -11.43     67.59
3DNA is unique in rigorously quantifying such differences using the six rigid-body bp parameters.

HTH,

Xiang-Jun

1177

General discussions (Q&As) / Re: question on +/- signs of local bp parameters

« on: January 11, 2013, 01:51:54 pm »

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

For B-DNA structures, some base-pair parameters (e.g., shear, opening) are normally quite small, so the difference between +/- values are not that obvious. For some extreme cases, however, the meaning in +/- is immediately obvious. For example, the famous U-G & G-U wobble pairs are distinguished by +/- shear -- see my post "Difference in shear of neighboring base pairs affects twist angle".

As for opening, if you could provide some concrete examples, I will help you work them through to see the difference.

HTH,

Xiang-Jun
 

1178

w3DNA -- web interface to 3DNA / Re: Structural quality

« on: January 11, 2013, 12:26:12 pm »

Hi Damien,

Please note that 3DNA works 'mechanically' -- it calculates a set of parameters for your input structure, without checking if it is reasonable at all. However, since an erroneous structure often gives some bizarre parameters, 3DNA can give a careful user some hint on possible issues.

A quick check using Jmol (or RasMol) shows one region of your model is displayed differently from the rest, signaling some problems. For a detailed report regarding the quality of your model, please try MolProbity (http://molprobity.biochem.duke.edu/).

Xiang-Jun

1179

General discussions (Q&As) / Re: Illegal instruction 4

« on: January 10, 2013, 12:02:14 pm »

Hi Susana,

Thanks for reporting the "Illegal instruction" error message when you ran 3DNA on your Mac OS X Lion 10.7.5 machine. It was due to a backward compatibility issue for the 3DNA binaries I compiled on a newer 10.8.x (Mountain Lion) Mac. I've recompiled 3DNA on a Mac OS X 10.6 (Snow Leopard) and now it should work for you; please download the 3DNA 2013jan10 version from the download page and report back how it goes.

I am using a MacBook Air as the primary machine to develop 3DNA, so a native Mac OS X version of the software should always be available.

HTH,

Xiang-Jun

1180

General discussions (Q&As) / Re: How to build a dsRNA helix with non-Watson-Crick base-pairs

« on: January 09, 2013, 08:33:43 pm »

3DNA does not provide an automatic way to build a dsRNA with non-Watson-Crick base pairs, e.g., the G-U wobble pair. Nevertheless, it has the components that can could possibly be combined to get the job done, on a case-by-case basis. If you are specific about what you want to achieve, our discussions can be more concerete. Alternatively, you may try software tools developed from the laboratories of Eric Westhof or François Major, among other possible choices.

Xiang-Jun

1181

w3DNA -- web interface to 3DNA / Re: misshapen base ring

« on: January 08, 2013, 01:19:16 pm »

Hi Damien,

I've updated 3DNA v2.1 to 2013jan08, with an improved algorithm for nucleotide identification. Specifically, in its default setting, DT8 on chain F is no longer recognized as a nucleotide. For the record, in my yesterday's response with an attached image, I observed the missing pair issue via Jmol using the DT8 as a test case. However, I did not check carefully to notice that previous versions of 3DNA, by virtue of very general distance cutoffs, actually take it as a nucleotide!

Note that the w3DNA web-server hosted at Rutgers is currently not yet updated to the latest version. So your best bet is to download the standard command-line version of 3DNA; it is the most efficient and convenient way to get your job done.

HTH,

Xiang-Jun

1182

w3DNA -- web interface to 3DNA / Re: misshapen base ring

« on: January 07, 2013, 01:34:38 pm »

Hi Damien,

Thanks for your follow-up. Yes, you can certainly use 3DNA to detect anomaly in a structure; that happened a (long) while ago at the NDB.

Thanks for pointing out the "bad" pair involving DT8 on chain F. The issue is due to the very 'generous' distance criteria used, which work well for 'reasonable' cases but apparently fail for your severely distorted structure. I'll fix the issue and update 3DNA shortly.

Xiang-Jun

1183

w3DNA -- web interface to 3DNA / Re: misshapen base ring

« on: January 07, 2013, 11:55:26 am »

Hi Damien,

Thanks for providing a sample PDB file that illustrates the problem you are facing; it helped me to identify the issue.

As shown by the attached image for DT8 on chain F, the base is distorted beyond recognition. For example, C5--C6 distance is only 0.42 Å -- far too short for a covalent bond, whereas N1--C6 = 1.97 Å and C4--C5 = 2.16 Å are far too long. So 3DNA won't recognize it as a DNA base T at all. Same issues exist for the other three nucleotides.

It does not makes much sense to change 3DNA to accommodate such erroneous cases; rather, the mistakes should be fixed in any tool you used to generate this structure in the first place.

HTH,

Xiang-Jun
 

1184

w3DNA -- web interface to 3DNA / Re: misshapen base ring

« on: January 07, 2013, 10:45:36 am »

Could you post (attach) an example structure to make your point concreate?

Xiang-Jun

1185

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 15, 2012, 12:14:16 pm »

The updated 3DNA v2.1 (2012dec15) should do the trick for you. In particular, I added the -ring option to 'analyze' and the corresponding 'x3dna_ensemble analyze' script. By default, the -ring option is not set for back compatibility. So other users won't notice any differences.

For example, in directory $X3DNA/examples/ensemble/md, you can run the following command:

x3dna_ensemble analyze -b bpfile.dat -e sample_md0.pdb -r

Note the -r option (short-hand form for -ring).

When you run x3dna_ensemble extract -l, you will find the new parameters are named as below:

Code: [Select]

[ 5] b1c_xyz             [ 6] b1n_vec             [ 7] b2c_xyz             [ 8] b2n_vec
Please verify and report back how it goes.

Xiang-Jun

1186

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 13, 2012, 11:03:57 am »

What do you mean exactly by "position of center of bases"? Geometric center of all base atoms, or just ring atoms? I may consider to add such info that can meet your needs and fit into other parts of 3DNA.

Xiang-Jun

1187

General discussions (Q&As) / Re: Large value of ZpH and inclination for Z-DNA

« on: December 10, 2012, 08:55:22 pm »

Hi Paul,

Thanks for posting back. In addtion to what I said in my previous reply, please note that 3DNA caluclates local step and helical parameters which could thus be strongly influenced by regional distortions. The same argument is true for the derived Xp/Yp/Zp parameters and their corresponding helical variants. The situation is especially noticeable for Z-DNA, as in your case, where the repeating unit is two base pairs but the structure is analyzed the 'normal' way (as in A- and B-DNA).

Other users of the forum may want to comment on your questions. Did you also post your questions on the CCP4 mailing list?

Xiang-Jun

1188

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 10, 2012, 01:17:01 pm »

Hi Ali,

Thanks for providing a sample AMBER MD trajectory file (actg3_md.pdb) which allow me to trace where the problem is.

A portion of PDB ATOM record from the file is as below:

Code: [Select]

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM     11  N9  DA5     1       0.781  -4.705  -0.553  0.00  0.00             
ATOM     12  C8  DA5     1      -0.573  -5.051  -0.401  0.00  0.00             
ATOM     13  H8  DA5     1      -0.879  -6.079  -0.526  0.00  0.00             
ATOM     14  N7  DA5     1      -1.349  -3.982  -0.328  0.00  0.00             
ATOM     15  C5  DA5     1      -0.421  -2.977  -0.164  0.00  0.00             
ATOM     16  C6  DA5     1      -0.512  -1.582   0.086  0.00  0.00       
According to the PDB format specification, columns 55 to 60 [Real(6.2)] is for atom occupancy. Normally, it is 1.00 -- check one of PDB entries (e.g., 355d) for an example. Now, as you can see, AMBER puts 0.00 there. It happens that in the 2012dec09 release of 3DNA, I added checking for atom occupancy (see "What's new?" for details). It is in that release that atoms with zero occupancy are ignored -- so find_pair would judge that your MD trajectories contains no base pairs. That explains your observation:

By the previous release (2012Nov26) there is not any problem!

You raised an interesting question:

Is it not possible that 3DNA analyze directly the output trajectory file of famous MD codes such as Amber?

Surely I'll like to make 3DNA directly applicable to the output trajectory file of the famous AMBER package. So I have now made checking for -occupancy optional that can be turned on by user explicitly. Download the updated 3DNA v2.1 2012dec10 release, and it should have solved the problem.

Xiang-Jun

1189

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 10, 2012, 08:02:48 am »

Thanks for letting me know the new issues you experienced -- I will look not them and get back to you shortly.

Xiang-Jun

1190

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 09, 2012, 08:48:26 pm »

Hi Ali,

Thanks for clarifying your question and providing further details on what you aim to achieve.

Following my previous reply, I've revised the Ruby script associated with x3dna_ensemble to parse the section "Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in the coordinate system of the given structure". The two newly-added parameters to extract are: bpo_xyz and bpn_vec. Please download 3DNA v2.1(2012dec09) and let me know if that fits the bill.

Since you are interested in base stacking interactions, your may also want to check the section "Overlap area in Angstrom^2 between polygons defined by atoms on successive bases. Polygons projected in the mean plane of the designed base-pair step."

HTH,

Xiang-Jun

1191

MD simulations / Re: Base stacking from x3dna_ensemble

« on: December 08, 2012, 08:48:13 pm »

Hi Ali,

Thanks for using 3DNA and posting your questions on the forum. With feedbacks from users like you, 3DNA can only become more useful to the community.

I think I understand your question: the 3DNA analyze program includes a section as below:

****************************************************************************
Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in
   the coordinate system of the given structure

      bp        Ox        Oy        Oz        Nx        Ny        Nz
    1 C-G      17.13     25.96     25.88     -0.10     -0.44     -0.89
    2 G-C      16.56     24.81     22.95     -0.21     -0.33     -0.92
    3 C-G      16.16     23.97     19.28     -0.18     -0.48     -0.86
...........................................................................

However, the parameters herein are not in x3dna_ensemble output. Am I right?

That section is currently not parsed by the x3dna_ensemble script -- you are the first to make this request. I will consider to add the portion in x3dna_ensemble output in the next release of 3DNA v2.1(beta) in the near future. What format do you prefer?

Xiang-Jun

1192

General discussions (Q&As) / Re: Large value of ZpH and inclination for Z-DNA

« on: December 03, 2012, 12:10:56 am »

Hi paul,

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

As detailed in the 2003 3DNA NAR paper, the set of helical parameters (X-disp, Y-disp, h-Rise, Incl., Tip, h-Twist) parallels that of the stacking parameters (Shift, Slide, Rise, Tilt, Roll, Twist); each represents a rigorous mathematical description of the relative geometry (position and orientation) of the two base pairs involved. You can verify the parameters by rebuilding an atomic model using the output file "bp_helical.par" -- the RMSD of base atoms between 3DNA rebuilt structure and the original one should be virtually zero.

From your list of the parameters, it's clear that two CG/CG steps differ from each other: what is the RMSD between them? Do you see "something specific" there by using a visualization tool (PyMOL/Jmol)? As always, 3DNA outputted parameters should be checked along with other means and your understanding of your structure to make "sense".

As elaborated in the thread "A-DNA definition" on the forum, the Zp vs ZpH parameters are mainly used to distinguish right-handed A-, B- and TA-DNA forms. I have not checked how the ZpH values vary in left-handed Z-DNA.

Z-DNA has dinucleotide as a repeating unit, so you need to add (-6 + -54) or analyze alternating base pairs to get the ~-60° twist angle.

To get started with DNA structures, I highly recommend the book "Understanding DNA: The Molecule and How it Works" by Calladine. You may check publications by Dr. Remo Rohs on DNA shape (minor groove width).

HTH,

Xiang-Jun

1193

RNA structures (DSSR) / Re: Can 3DNA be used to build a miRNA-target structure?

« on: November 21, 2012, 12:25:59 pm »

Hi Guido Leoni,

Thanks for providing such a detailed explanation of your miRNA-mRNA pairment question. I can now clearly see what you want to achieve, and I understand the importance of your research area.

Am I right to assume that the RNA structure you want to build is (with code tag for monospace)?

Code: [Select]

U A A A G U G C U U A U
| | | | | | | |     | |
A U U U C A C G C C U A

There are many tools dedicated to building three-dimensional RNA structures, see for example "RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction". You may want to check some of the tools included in the evaluation paper, or try other (newer) ones.

If you want to try out 3DNA, here are the procedures to build an approximate structure with the above sequence and secondary structure:

# build an RNA duplex with Watson-Crick base pairs
fiber -se=UAAAGUGCUUAU -r RNA-WC-duplex.pdb
find_pair RNA-WC-duplex.pdb stdout
# as shown below:
NA-WC-duplex.pdb
RNA-WC-duplex.out
    2         # duplex
   12         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   24  0 #    1 | ....>A:...1_:[..U]U-----A[..A]:..24_:B<....  0.11  0.06 10.52  8.94 -4.24
    2   23  0 #    2 | ....>A:...2_:[..A]A-----U[..U]:..23_:B<....  0.11  0.06 10.52  8.94 -4.24
    3   22  0 #    3 | ....>A:...3_:[..A]A-----U[..U]:..22_:B<....  0.11  0.06 10.52  8.94 -4.24
    4   21  0 #    4 | ....>A:...4_:[..A]A-----U[..U]:..21_:B<....  0.11  0.06 10.51  8.94 -4.24
    5   20  0 #    5 | ....>A:...5_:[..G]G-----C[..C]:..20_:B<....  0.24  0.07 10.52  8.94 -4.10
    6   19  0 #    6 | ....>A:...6_:[..U]U-----A[..A]:..19_:B<....  0.11  0.06 10.52  8.95 -4.24
    7   18  0 #    7 | ....>A:...7_:[..G]G-----C[..C]:..18_:B<....  0.24  0.07 10.52  8.94 -4.09
    8   17  0 #    8 | ....>A:...8_:[..C]C-----G[..G]:..17_:B<....  0.24  0.07 10.52  8.95 -4.10
    9   16  0 #    9 | ....>A:...9_:[..U]U-----A[..A]:..16_:B<....  0.11  0.06 10.52  8.94 -4.24
   10   15  0 #   10 | ....>A:..10_:[..U]U-----A[..A]:..15_:B<....  0.11  0.06 10.52  8.94 -4.24
   11   14  0 #   11 | ....>A:..11_:[..A]A-----U[..U]:..14_:B<....  0.11  0.06 10.52  8.94 -4.24
   12   13  0 #   12 | ....>A:..12_:[..U]U-----A[..A]:..13_:B<....  0.11  0.06 10.52  8.94 -4.24
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (12): 1 - 12

# now mutate A15 and A16 on chain B to C
mutate_bases 'c=B s=16 m=C; c=B s=15 m=C' RNA-WC-duplex.pdb RNA-ok-duplex.pdb
find_pair RNA-ok-duplex.pdb stdout
# now you get the desired miRNA-mRNA duplex with two U--C mis-matches: 
RNA-ok-duplex.pdb
RNA-ok-duplex.out
    2         # duplex
   12         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   24  0 #    1 | ....>A:...1_:[..U]U-----A[..A]:..24_:B<....  0.11  0.06 10.52  8.94 -4.24
    2   23  0 #    2 | ....>A:...2_:[..A]A-----U[..U]:..23_:B<....  0.11  0.06 10.52  8.94 -4.24
    3   22  0 #    3 | ....>A:...3_:[..A]A-----U[..U]:..22_:B<....  0.11  0.06 10.52  8.94 -4.24
    4   21  0 #    4 | ....>A:...4_:[..A]A-----U[..U]:..21_:B<....  0.11  0.06 10.51  8.94 -4.24
    5   20  0 #    5 | ....>A:...5_:[..G]G-----C[..C]:..20_:B<....  0.24  0.07 10.52  8.94 -4.10
    6   19  0 #    6 | ....>A:...6_:[..U]U-----A[..A]:..19_:B<....  0.11  0.06 10.52  8.95 -4.24
    7   18  0 #    7 | ....>A:...7_:[..G]G-----C[..C]:..18_:B<....  0.24  0.07 10.52  8.94 -4.09
    8   17  0 #    8 | ....>A:...8_:[..C]C-----G[..G]:..17_:B<....  0.24  0.07 10.52  8.95 -4.10
    9   16  0 #    9 | ....>A:...9_:[..U]U-**--C[..C]:..16_:B<....  0.11  0.06 10.52  8.99  0.76
   10   15  0 #   10 | ....>A:..10_:[..U]U-**--C[..C]:..15_:B<....  0.11  0.06 10.51  8.99  0.76
   11   14  0 #   11 | ....>A:..11_:[..A]A-----U[..U]:..14_:B<....  0.11  0.06 10.52  8.94 -4.24
   12   13  0 #   12 | ....>A:..12_:[..U]U-----A[..A]:..13_:B<....  0.11  0.06 10.52  8.94 -4.24
##### 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 1 helix (0 isolated bps)
##### Helix #1 (12): 1 - 12

Note that you need to use the current version of 3DNA v2.1 from the download page. For your reference, attached below are the two PDB files RNA-WC-duplex.pdb and RNA-ok-duplex.pdb mentioned above.

1194

w3DNA -- web interface to 3DNA / Re: O3'-P distance too long after reconstruction

« on: November 21, 2012, 11:20:27 am »

- The default O3'-P distance is 4.5A. From the ADIT server of the PDB, the expected value is 1.6A. What is in fact the range of the possible values?

The O3'-P covalent bond distance is ~1.6 A, as you noticed on the ADIT server of the PDB. The 3DNA default of 4.5 A is purely an empirical value used to decide if to include the bond in a corresponding CONECT record in the rebuilt PDB file; it has no 'chemical' meaning. Have a look of build.pdb file using a text editor, you will see my point.

- Could you indicate some tools alllowing to do energy minimization?

AMBER should help. Some other MD packages or Phenix should also do the trick. Yet, I still failed to find a command-line tool that can 'regularize' the backbone to a reasonable geometry while keeping the base atoms fixed.

HTH,

Xiang-Jun

1195

MD simulations / Re: analyzing longer DNA sequences

« on: November 21, 2012, 11:05:56 am »

I am not sure if this is too much to ask you.

No, it's not; I always welcome user questions such as this one, and I strive to be as helpful as I could.

Now I see the problem you are experiencing. Strictly speaking, and as I mentioned in my previous reply, it's not a 3DNA problem but at the interface between 3DNA and Curves+. Since the purpose of providing the find_pair c+ option is to build a bridge between the two commonly used software programs for analyzing nucleic acid structures, I'd like to dig the issue further to see if anything can be done from 3DNA's perspective.

Your Curves+ input file curves.inp, as generated with find_pair -c+, has the following content:

&inp file=sel.pdb,
     lis=sel,
     fit=.t.,
     lib=./standard,
     isym=1,
&end
    2    1   -1    0    0
    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24
   47   46   45   44   43   42   41   40   39   38   37   36   35   34   33   32   31   30   29   28   27   26   25

which has 23 base pairs (note that bases 1 and 48 are not paired). Yet when the file is fed to Curves+, only the first 15 bps are recognized.

Combined strands have   15 levels ...

  Strand  1 has  15 bases (5'-3'): GTGTGAGCGTGGGCG
  Strand  2 has  15 bases (3'-5'): CACACTCGCACCCGC

To help solve the problem, could you try the following and report back (in detail) what you get?

• Instead of 23 bps, shorten the list to < 15, say 10, as below:
  

      2    3    4    5    6    7    8    9   10   11
     47   46   45   44   43   42   41   40   39   38

  Run Curves+ on it again, do you get what you expect?
  
• Since the nucleotide numbers are continuous, you can use the short-hand form to specify paired bases:
  

      2:24
     47:25

  Run Curves+, what do you get?
  

Xiang-Jun

1196

RNA structures (DSSR) / Re: Can 3DNA be used to build a miRNA-target structure?

« on: November 21, 2012, 10:33:48 am »

Could you be more specific, better with an example (or reference), to illustrate exactly what want to achieve?

Xiang-Jun

1197

w3DNA -- web interface to 3DNA / Re: O3'-P distance too long after reconstruction

« on: November 21, 2012, 10:31:54 am »

Hi Damien,

The fact that "O3'-P distance too long after reconstruction" is well expected; 3DNA built structures are accurate for the bases, with only an approximate sugar-phosphate backbone. See FAQ "How do I build nucleic acid structures with sugar-phosphate backbone?"

For cases with longer than the default 4.5 A O3'(i)--P(i+1) distance, the 3DNA rebuild program outputs info message as below (using your example, and with a B-DNA backbone conformation):

Code: [Select]

O3' (#317) and P (#331) on chain A have distance 5.3 over 4.5: no linkage assigned
O3' (#768) and P (#782) on chain B have distance 5.2 over 4.5: no linkage assigned
This approximate structure may serve as a starting point for energy minimization.

Xiang-Jun
 

1198

MD simulations / Re: analyzing longer DNA sequences

« on: November 20, 2012, 04:29:58 pm »

Hi Shyno,

Thanks for providing details of the commands you used and attaching three relevant files. However, I fail to see what're wrong here; things are working as expected from my understanding.

With the -c+ option, you get what's desired, as in your attached curves.inp file. Running find_pair in its default settings on your PDB file sel.pdb gives expected results:

find_pair sel.pdb stdout
sel.pdb
sel.out
    2         # duplex
   23         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    2   47  0 #    1 | ....>A:...2_:[..G]G-----C[..C]:..48_:B<....  0.77  0.76 28.01  8.85 -1.31
    3   46  0 #    2 | ....>A:...3_:[..T]T-----A[..A]:..47_:B<....  0.32  0.02 11.50  9.26 -4.07
    4   45  0 #    3 | ....>A:...4_:[..G]G-----C[..C]:..46_:B<....  0.83  0.64  4.42  9.11 -2.68
    5   44  0 #    4 | ....>A:...5_:[..T]T-----A[..A]:..45_:B<....  0.54  0.32 21.12  8.91 -2.76
    6   43  0 #    5 | ....>A:...6_:[..G]G-----C[..C]:..44_:B<....  0.45  0.27 27.61  8.88 -2.64
    7   42  0 #    6 | ....>A:...7_:[..A]A-**+-T[..T]:..43_:B<....  3.71  0.96 28.75  7.04  4.07
    8   41  0 #    7 | ....>A:...8_:[..G]G-----C[..C]:..42_:B<....  0.45  0.32  3.39  8.97 -3.75
    9   40  0 #    8 | ....>A:...9_:[..C]C-----G[..G]:..41_:B<....  1.05  0.47  8.17  8.82 -2.61
   10   39  0 #    9 | ....>A:..10_:[..G]G-----C[..C]:..40_:B<....  0.76  0.50 21.19  8.86 -2.17
   11   38  0 #   10 | ....>A:..11_:[..T]T-----A[..A]:..39_:B<....  0.34  0.27  5.44  9.01 -3.84
   12   37  0 #   11 | ....>A:..12_:[..G]G-----C[..C]:..38_:B<....  0.58  0.48 12.17  9.02 -2.85
   13   36  0 #   12 | ....>A:..13_:[..G]G-----C[..C]:..37_:B<....  0.24  0.03 16.54  9.08 -3.88
   14   35  0 #   13 | ....>A:..14_:[..G]G-----C[..C]:..36_:B<....  0.69  0.69 14.12  9.14 -2.22
   15   34  0 #   14 | ....>A:..15_:[..C]C-----G[..G]:..35_:B<....  0.41  0.09 14.35  9.02 -3.70
   16   33  0 #   15 | ....>A:..16_:[..G]G-----C[..C]:..34_:B<....  0.40  0.39 26.56  9.03 -2.49
   17   32  0 #   16 | ....>A:..17_:[..T]T-----A[..A]:..33_:B<....  0.70  0.62  8.01  9.49 -2.65
   18   31  0 #   17 | ....>A:..18_:[..A]A-----T[..T]:..32_:B<....  0.26  0.21 18.44  8.96 -3.41
   19   30  0 #   18 | ....>A:..19_:[..C]C-----G[..G]:..31_:B<....  0.26  0.09 25.81  9.27 -3.27
   20   29  0 #   19 | ....>A:..20_:[..A]A-----T[..T]:..30_:B<....  0.63  0.21 19.54  8.96 -2.98
   21   28  0 #   20 | ....>A:..21_:[..C]C-----G[..G]:..29_:B<....  0.57  0.33  6.64  9.06 -3.43
   22   27  0 #   21 | ....>A:..22_:[..A]A-----T[..T]:..28_:B<....  1.09  1.01 10.89  8.63 -1.34
   23   26  0 #   22 | ....>A:..23_:[..C]C-----G[..G]:..27_:B<....  0.66  0.37 28.93  9.04 -2.16
   24   25  0 #   23 | ....>A:..24_:[..A]A-----T[..T]:..26_:B<....  2.72  2.29 25.44  7.75  5.57
##### 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 (23): 1 - 23

Certainly, find_pair is working properly, as designed. Is there anything I am missing here?

Xiang-Jun

1199

MD simulations / Re: analyzing longer DNA sequences

« on: November 20, 2012, 02:22:59 pm »

Hi Shyno,

DNAs with 62 base pairs should not be a problem for 3DNA to analyze; specifically, find_pair and other 3DNA components have no default bp limit other than your computer's memory.

As always, please be specific by providing a reproducible example; that will help solve your problem.

Xiang-Jun

1200

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

« on: November 11, 2012, 11:00:52 pm »

Thanks for posting your problem on installing 3DNA. Am I right to assume that your system is Windows with MinGW/MSYS? Could you be more specific about your Windows systems -- XP, Vista or Windows 7? Is it 32 bit or 64 bit?

Xiang-Jun