Messages

1476

General discussions (Q&As) / Re: findpair -p and -z options

« on: March 12, 2010, 08:53:09 pm »

Hi Pascal,

The "-p" option of find_pair is for pairwise checking of all possible base-pairs, and for identifying higher-order base associations as demonstrated in the 2008 3DNA NP paper (Recipe no. 5). It was not intended to be used with analyze, as I initially added the option there. The "-z" option, on the other hand, was mostly used to decide suitable criteria of which base-pair should be included in a helical region. Its output information is far too technical for outside users.

Regarding the output parameters from the "-p" option, the header section should be of some help:
[pre:byvny7l4]Six-line information for each base-pair as follows:
   #1: Overall serial number, local serial number, paired residue numbers,
       detailed pairing residue information.
   #2: One-letter base-pair followed by six base-pair parameters (shear,
       stretch, stagger, buckle, propeller, opening). The parameters are
       with respect to the Watson-Crick base reference frame. There are
       two types of base-pair orientation: M-N means the two bases have
       opposite orientations as in Watson-Crick base-pair; M+N means the
       two bases have the same local orientations as in Hoogsteen base-
       pair. All possible base pairing patterns can then be classified
       based on the six parameters, among which shear, stretch and opening
       are most discriminative.
   #3: H-bonding information (atom pair followed by their distance).
   #4: Overall classification of the base-pair (anti-parallel vs parallel
       based on relative z-axis of the two bases, cis vs trans based on
       x-axis and C1-RN9/YN1 directions).
   #5: Relative directions of the three axes and their numerical values.
       The last 3 numbers are the angles between the glycosidic bonds, and
       the two chi torsion angles.
   #6: The actual parameters used to locate the base-pair in question.[/pre:byvny7l4]
Some of the undocumented features of 3DNA are experimental or are related to still unpublished work. I am hoping to be able to devote more efforts to research on nucleic acid structures, but it all depends.

Xiang-Jun
[hr:byvny7l4][/hr:byvny7l4]
PS. BTW, isn't FR3D sufficient for tasks related to the identification and classification of base-pairs? The FR3D webpage contains tons of information; some of which you may find helpful.

1477

General discussions (Q&As) / Re: Finding non-sequential base step parameters

« on: March 08, 2010, 07:53:39 pm »

I am wondering if it's possible to find all base step parameters

No, it is not possible. There are simply too many possibilities, e.g., for 23S rRNA in 1jj2, and most of them make no sense at all.

I am aware that I can isolate the base_step and calculate the step parameters for them

What do you mean to "isolate the base_step"? If you separate find_pair -s from analyze, you could simply play with the output file from the former to get what you want.

HTH,

Xiang-Jun

1478

General discussions (Q&As) / Re: Error Running X3DNA_setup script

« on: February 01, 2010, 11:11:23 pm »

The Perl script x3dna_setup is a simple, straightforward utility program with source code available. Apparently, you are more a Windows users, not that familiar with Linux/Unix and Perl. So it would be most helpful if you could find a local expert to help you out.

Here are some specific suggestions:

• Is x3dna_setup executable? You may need to run "chmod u+x *" in X3DNA/bin/ directory.
• What "which perl" outputs? If not /usr/bin/perl, you will need to change the first line in the script to reflect your local setting.
• Does your Perl installation have modules "FindBin" and "File::Basename"? If not, you will need to have then installed.
• What is the output of the following:
  
  Code: [Select]
  echo $HOME
echo $SHELL
and the directory of you 3DNA installation?

Since I am basically a non-Windows person, I am hoping other 3DNA users using Cygwin and MinGW would help out with more detailed instructions.

Xiang-Jun

1479

General discussions (Q&As) / Re: RNA 2D structure

« on: January 24, 2010, 07:28:38 pm »

I would like to get the secondary structure of all these 3D structures. Is it possible with 3DNA software? If so please let me know how to use that.

From a 3D RNA structure in PDB format, find_pair in 3DNA can identify all the double helical regions. Maybe that would serve as a starting point?

You may also find my blog post titled "Does 3DNA work for RNA?" relevant.

HTH,

Xiang-Jun

1480

General discussions (Q&As) / Re: 3DNA

« on: January 23, 2010, 08:36:27 pm »

Hi I buy the software 3DNA AND I can not access the download add-on WORLD, can you help me :roll:

Where did you buy "the software 3DNA" :? ? This 3DNA forum is on "Topics Related to the 3DNA Software Package for the Analysis, Rebuilding & Visualization of Three-dimensional Nucleic Acid Structures", and it does not have "add-on WORLD" at all.

Xiang-Jun

1481

General discussions (Q&As) / Re: DNA Step Values for DNA Mismatches

« on: January 21, 2010, 10:33:57 pm »

...... reading file: baselist.dat ......
unknown residue DG 1 on chain E [#1]
Check the base and add one more item in file <baselist.dat>

Take the hint, and read FAQs on "How to fix missing (superfluous) base pairs identified by find_pair?" and "How to handle modified (uncommon) bases?" to see how to handle such cases.

Notice that it complains about the DG residue. As well, it is unable to produce the corresponding 2O8B.out file. I think that this is due to the unrecognized naming convention "DG" which should be written as "GUA" instead. This is why I had extracted the coordinates before and renamed them all to GUA, ADE, THY, and CYT.

Following the suggestion above, you do not need to manipulate PDB file at all. 3DNA v1.5 works in such situation as well, and this topic has been brought up in the forum before.

...... reading file: baselist.dat ......
uncommon residue ADP 936 on chain A [#1793] assigned to: a
uncommon residue ADP 202 on chain B [#1795] assigned to: a
................................................................
Instead of complaining about the DG (which I assume is "fixed" in v2.0), it complains about the ADP nucleotides which are present in the PDB file (of 2O8B.pdb, not the modified one).

Note that this is for information only. Again, reading and understanding the above mentioned two FAQs would help.

ii) They both still do NOT contain the first G-C base pair information (even with v2.0 using an unmodified PDB file downloF:..30_:[.DC]Caded from PDB.org).

I have just checked and reproduced your result with the distributed 3DNA v2.0. The missing first G-C base-pair is due to the distortion of C30 on chain F.

iii) The output format for v2.0 is slightly different from v1.5 (so my parsing script written in Perl will need to be modified)

iv) The final column in each row for each base step is different (-1.13 vs. 1.03). I think I read somewhere that this value is simply being calculated differently?

v) The base-pair criteria used appears slightly different.

Over the time, there are some internal changes in find_pair. Moreover, contents following "#" are for information only, undocumented, and are subjected to changes.

4) I will try modifying the helix break parameter as you had suggested (just for experience) but from what you said, it looks like I could just extract the pertinent information directly from the "bp_step.par" file without having to do that since it will always include a complete set of parameters. Is that correct?

If you are just interested in getting the numbers, yes, 'bp_step.par' contains all the base-pair and step parameters.

HTH,

Xiang-Jun

1482

General discussions (Q&As) / Re: DNA Step Values for DNA Mismatches

« on: January 17, 2010, 05:45:42 pm »

Hi Sean,

Thanks for the well-formulated question. I am impressed that you noticed the fact that a set of step parameters is omitted in 3DNA main parameters file (*.out) of 2o8b, but available in file 'bp_step.par'. In my support of 3DNA over the years, you are the first who has dug into this detail.

First, a clarification:

After extracting the DNA coordinates and analyzing it with 3dna, ...

Did you that you do not need to first perform "extracting the DNA coordinates" from the PDB file? With "find_pair", you can analyze a nucleic acid structure directly from a PDB file. See FAQ for an example.

Now to your specific questions:

Code: [Select]

5 GC/GC -0.20 0.24 3.45 2.85 -2.55 38.63
6 CG/TG ---- ---- ---- ---- ---- ----
7 GC/GT 3.87 0.83 3.32 -11.26 0.08 6.18I should point out that step 6 is where the G-T mismatch is located but I don't understand why the parameter values are missing.

If you check carefully the output file from "find_pair" (BTW, your output file apparently lacks the first G-C base-pair, why?),

Code: [Select]

2o8b.pdb
2o8b.out
    2         # duplex
   15         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   30  0 #    1 | ....>E:...1_:[.DG]G-----C[.DC]:..30_:F<....  1.14  0.36 14.09  9.30 -0.44
    2   29  0 #    2 | ....>E:...2_:[.DA]A-----T[.DT]:..29_:F<....  0.89  0.82 26.82  9.09 -1.13
    3   28  0 #    3 | ....>E:...3_:[.DA]A-----T[.DT]:..28_:F<....  0.23  0.03 18.38  9.24 -3.78
    4   27  0 #    4 | ....>E:...4_:[.DC]C-----G[.DG]:..27_:F<....  0.78  0.19  8.59  8.93 -3.40
    5   26  0 #    5 | ....>E:...5_:[.DC]C-----G[.DG]:..26_:F<....  0.56  0.29 17.33  9.24 -3.00
    6   25  0 #    6 | ....>E:...6_:[.DG]G-----C[.DC]:..25_:F<....  0.29  0.27 19.28  9.01 -3.20
    7   24  9 #    7 x ....>E:...7_:[.DC]C-----G[.DG]:..24_:F<....  0.22  0.01 24.18  9.04 -3.55
    8   23  0 #    8 | ....>E:...8_:[.DG]G-**--T[.DT]:..23_:F<....  5.22  0.31 43.28  9.87  7.00
    9   22  0 #    9 | ....>E:...9_:[.DC]C-----G[.DG]:..22_:F<....  0.44  0.33 20.98  8.84 -2.85
   10   21  0 #   10 | ....>E:..10_:[.DG]G-----C[.DC]:..21_:F<....  0.41  0.39 10.80  9.05 -3.28
   11   20  0 #   11 | ....>E:..11_:[.DC]C-----G[.DG]:..20_:F<....  0.26  0.01 12.86  9.06 -4.07
   12   19  0 #   12 | ....>E:..12_:[.DT]T-----A[.DA]:..19_:F<....  0.85  0.47 11.88  8.95 -2.62
   13   18  0 #   13 | ....>E:..13_:[.DA]A-----T[.DT]:..18_:F<....  0.53  0.18  9.30  8.85 -3.65
   14   17  0 #   14 | ....>E:..14_:[.DG]G-----C[.DC]:..17_:F<....  1.17  0.94 21.28  8.97 -0.89
   15   16  0 #   15 | ....>E:..15_:[.DG]G-----C[.DC]:..16_:F<....  1.17  0.05 37.85  8.66 -1.83
##### 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 2 helices (0 isolated bps)
##### Helix #1 (7): 1 - 7
##### Helix #2 (8): 8 - 15
you will find that the structure has been broken into two helical fragments, at the middle G-T pair. If you set the helix_break parameter in file 'misc_3dna.par' (see the FAQ) from the default 7.5 Å to a larger value, e.g., 8.5 Å as below (3DNA v2.0),

Code: [Select]

#   distance criterion for helix break
<helix_break>8.5</helix_break>"find_pair" will take the whole double helix as a single unit, and the "analyze" output parameters would have included the "missing" step.

Alternatively, with default 'misc_3dna.par' parameters, you can still recover the "missing" step parameters by adding '-c' option to "analyze". Type "analyze -h" to see how it works, and yet another alternative.

In addition, I notice that another output file (bp_step.par) that contains the base-pair step parameters actually has values for the mismatch:
.............................
The (shift, slide, rise, tilt, roll) values are essentially identical in both cases with the exception of the missing values for the mismatch. What do the values in the latter case actually mean and why are they missing in the first case?

No matter how many helical regions are involved in the input file to "analyze", the fixed-named output file 'bp_step.par' always include a compete set of parameters, including the inter-helix steps. This is to ensure that "rebuild" has enough information to construct a model of the whole structure. Thus, the values in the two cases (*.out vs "bp_step.par") mean exactly the same thing; they just serve two different purposes.

HTH,

Xiang-Jun

1483

SCHNAaP/SCHNArP / Re: backbone utility program

« on: January 06, 2010, 08:49:12 pm »

I am glad that you find my SCHNArP program useful to your project.

The 1997 publication on SCHNArP mentions that there is a utility that "traces the path of the backbone by connecting the C1' or RN9/YN1 atoms in the atomic models and the sugar atoms in the schematic models." I cannot locate that utility program in the SCHNAaP/SCHNArP package.

The connection is for visualization purpose only, i.e., to help "traces the path of the backbone". As far as I can recall, the utility was initially written in Matlab, and was intended to be with used with Rasmol. The atomic models in PDB format normally do not contain explicit bond connections. So in the C version distributed, I decided to support this functionality only for the schematic models in Alchemy format; it is now integrated into SCHNArP directly.

For your verification, in the Examples/ directory, you will find several example files DNAp76[a-d].cnt which contain such "backbone" trace. I have also just run SCHNArP using DNAp76a.dat as input, and got two files: CEHS_gen.cnt and CEHS_gen.out. The attached image corresponds to CEHS_gen.cnt. It was generated with Rasmol 2.6.4. (see my blog post: http://xiang-jun.blogspot.com/2009/06/r ... sayle.html)

Note that the file DNAp76a.cnt was generated using a different base-pair BLOCK model. See README.1st and options available in BaseGeo/BLOCK*.alc files; feel free to play with it.

Also, are there source codes available that provide atomistic coordinates of the backbone sugar/phosphate atoms between 2 existing bases?

There must be such source codes available somewhere, but not in SCHNArP or 3DNA. In my understanding, given the geometry of two bases or base-pairs, there is no unique/object ways to define the backbone conformation. So in SCHNArP/3DNA, I've only provided simple rigid-body A-, or B- conformations, attached to the bases. Such approximate full atomic models with backbone could be useful as starting points for other explorations (see our 3DNA 2008 Nature Protocols paper for further explanation on this topic).

HTH,

Xiang-Jun

1484

General discussions (Q&As) / Re: Deformability of a small DNA fragment

« on: November 23, 2009, 11:38:31 pm »

3DNA does not perform energy calculations per se, but please have a look of the post "deformation energy calculation program" by Dr. Thomas Gaillard at the Users' contributions section.

If you have further technical questions, you may want to post over there: I think Dr. Gaillard would follow up.

Xiang-Jun

1485

General discussions (Q&As) / Re: From DNA sequence to DNA structure

« on: November 19, 2009, 08:23:13 pm »

The basic issue is that there is no one-to-one correspondence between DNA sequence and its 3D structure. For example, a 146-bp fragment could be in left-handed super-helical form as in nucleosomal DNA,  or other other conformations (straight or not). In the literature, there have been several bending models, each of which assigns a set of step parameters (roll, twist etc) to specific sequence (at di-, tri- or tetra-nucleotide level).

As noted in the 3DNA 2008 Nature Protcols paper (3DNA-NP):

"Thirdly, as demonstrated in SCHNArP, various DNA bending ‘rules’, with different sets of tilt/roll/twist values at the constituent dinucleotide or trinucleotide steps, can be easily incorporated within a script that transforms a sequence with an assigned ‘bending model’ into an input file that feeds into rebuild."

So overall, you are in the right direction, as far as building a DNA model is concerned. Now to your specific questions:

1. I used only dinucleotide shift, slide, rise, tilt, roll and twist parameters that download from DiProDB, but ignored Shear, Stretch, Stagger, Buckle, Prop-Tw and Opening.

The "rebuild" program in 3DNA can take two types of input, as documented in 3DNA-NP. You can ignore Shear, Stretch ... etc base-pair parameters, which will be taken as zeros.

2. I wrote a small program to generate a base step parameter file from DNA sequence just like the bp_step.par in X3DNA example.

It can be simpler, as noted above. Please see also 3DNA-NP: working through recipe #2 would clarify the issues.

3. I use rebuild program to build a 3D model by using the base step parameter file in step 2. (rebuild -atomic M1_sense.3dna M1_sense.3dna.pdb)

Yes, it is right.

Everything works fine. But when I use SPDB Viewer to visualize my model, I found some segment did not connected well (please see Picture 2.png in attached file). Is this problem can be fixed?
Or this is a viewer problem? I've tried JMol, but Jmol cannot show it properly.

That's normal. Again as noted in 3DNA-NP:

Secondly, rebuild allows for the construction of atomic-level nucleic-acid structures (‘-atomic’ option) with sugar–phosphate backbones in pre-assigned, fixed conformations (specified by standard residue files; see the FAQ section at the 3DNA website). Such models, which have precise base-pair geometry but approximate (sometimes distorted) backbone connections, provide a useful starting point and basis for analysis of all-atom simulations.

One more note, 'rebuild' generated PDB files have full CONECT records, and should display with all proper connections with RasMol. Of course, some of the O3'(i) to P(i+1) bonds would be quite long.

So, I would suggest you to download 3DNA v2.0, and play with the worked examples.

HTH,

Xiang-Jun

1486

General discussions (Q&As) / Re: NUPARM vs X3DNA twist values

« on: November 11, 2009, 08:44:18 pm »

As illustrated in Figure 3 of the standard reference frame paper [J. Mol. Biol. 313(1), 229-237, 2001], and in the section "Treatment of non-Watson±Crick base pairing motifs" of the 3DNA 2003 NAR paper (also Figure 3), the discrepancy you noticed in Twist angle between 3DNA and NUPARM is due to large Shear of the G-U Wobble pairs.

You may need to (re)read the two papers for further details. It would be helpful if you repeat your calculations with Curves+ and post back your results: I would guess that Curves+ twist angle be pretty similar to that from 3DNA.

HTH,

Xiang-Jun

PS: Please also see my blog post "How shear affects twist angle of a dinucleotide step?"

1487

General discussions (Q&As) / Re: About DNA contour length

« on: October 30, 2009, 08:57:38 pm »

I have a question when calculating the DNA contour length. Can I use the sum of Rise as the contour length and use the sum of h-Rise as the end-to-end distance? So DNA bending is measured by the ratio of the end-to-end distance and the contour length?

3DNA does not calculate DNA contour length. As far as if it is appropriate to use sum of Rise as contour length, and sum of h-rise as end-to-end distance, why not you try some examples? Using ribosomal DNA superhelix, for example, would the numbers make sense? For quantify DNA bending, there are already discussions in the 3DNA forum. You could also try Curves/Curves+ from Lavery et al.

The other question is how to analyze a pdb file that has a lot of frames in it?

I do not think I understand your point here. Could you be more specific?

Xiang-Jun

1488

General discussions (Q&As) / Re: DNA rotation cont'd

« on: October 17, 2009, 06:31:48 pm »

As I said last time on Wed Jul 08, 2009, which is quoted below:

Could you be more specific? Which command and options did you use? Preferably with a reproducible example?

Unless you provide something specific and reproducible, I honestly do not know what you are talking about. When you claim something "not work", please provide a step-by-step description what have you done (which version, program and command-line options), and what error message you received, with all necessary data files and scripts. At the concrete level, it is easy to judge something right or wrong, and I always welcome 3DNA bug reports. In my experience, failing to provide a (minimal and) producible example and not being responsive are two of the top reasons that make a online forum discussion topic difficult and unproductive.

Please read carefully README First, and the note I sent with your forum registration.

Xiang-Jun

1489

General discussions (Q&As) / Re: 3DNA calculation for Bases that have two conformers in pdb

« on: October 08, 2009, 06:58:09 pm »

This is a subtle point with regard to the ATOM or HETATM records of PDB format, and I am glad that you raised the issue. 3DNA has been designed with this in mind and works as it should.

In 3DNA v2.0, file misc_3dna.par contains the following section:

Code: PHP

1. <span class="syntaxdefault"></span><span class="syntaxcomment"># Section 2&#58; alternative location in ATOM or HETATM records
2. #   default to A or 1 (A1), and ' ' is always added
3. </span><span class="syntaxkeyword"><</span><span class="syntaxdefault">alt_list</span><span class="syntaxkeyword">></span><span class="syntaxdefault">A1</span><span class="syntaxkeyword"></</span><span class="syntaxdefault">alt_list</span><span class="syntaxkeyword">></span><span class="syntaxdefault"> </span>

Thus, by default, only ATOM or HETATM records with alternative locations (column #17) of ' ', 'A' or '1' are processed. Of course, as pointed out in 3DNA FAQ, you could modify file misc_3dna.par to use other alternative locations: 'B', for example.

HTH,

Xiang-Jun

PS:

• Every 3DNA user should upgrade to v2.0: you have nothing to lose (no backward compatibility issues) but to take advantage of a more refined piece of software.
  
• Are you sure 437D.pdb has the ATOM records you listed?
  
  Code: [Select]
  e.g from 437D.pdb
ATOM 47 O4'A G A2648 -26.371 52.168 -12.884 0.58 13.58 O
ATOM 48 O4'B G A2648 -25.879 52.221 -11.854 0.42 16.38 O
ATOM 49 C3'A G A2648 -24.982 50.605 -13.934 0.58 11.81 C
ATOM 50 C3'B G A2648 -24.120 50.873 -12.569 0.42 14.39 CI cannot find them in 437D.pdb. It is not an important point here, but it would be helpful if you can clarify the discrepancy, just for the record.

1490

General discussions (Q&As) / Re: Option not to display calculation status to screen.

« on: September 02, 2009, 11:28:37 pm »

Hi Mauricio,

Thanks for formulating your question so clearly, especially for providing an example. Browsing the forum, one would find how many times I have asked for clarifications so I can understand what a question is about, exactly.

Okay, now back to your question.

Ideally, I could have provided a -q option (for quiet, or something similar) so the output message can be suppressed. As current is with 3DNA, however, the diagnostic information is directed to stderr. This should not be a problem in real life, with the help of Unix/Linux file redirection.

Again, an example would make the point clear. So let's use 'bdl084.pdb', you need to do the following:

Code: [Select]

find_pair bdl084.pdb bp_info 2> msg1
analyze bp_info 2> msg2

# or by combining them as this
find_pair bdl084.pdb stdout 2> msg1 | analyze 2> msg2
Note I am using bash shell. For other shells, you may need to use something different. Of course, you could also play with some variants along the line.

HTH,

Xiang-Jun

1491

General discussions (Q&As) / Re: trajectory analysis: error with analyze

« on: August 05, 2009, 08:50:16 pm »

I figured out an error with my simulations - I hadn't taken care of PBC. So, after fixing it I no longer get the error I had mentioned.

However, I would still like to know a bit more about the error.

I am glad that you figured out where the problem was.

Regarding the meaning of the error message,

Code: [Select]

some residue has more than one pair
residue index 24 too big (> 22)
please check your input fileIt would help clarify the issue greatly if you include a minimal, producible example so others can understand exactly what you mean. Broadly speaking, it means the input file to analyze does not match the corresponding PDB file. More specifically, in your input file, a nucleotide is specified with sequential no. 24, while the PDB has only 22 residues.

HTH,

Xiang-Jun

1492

General discussions (Q&As) / Re: 3DNA version 2.0

« on: July 27, 2009, 07:46:17 pm »

Thanks for your interest in 3DNA and for sharing your difficult experience with the user community. Over the past few months, I have received (being CC-ed) dozens of email requests for 3DNA v2.0, and I am just wondering if anyone has a more positive story to cheer up the mode of this thread a bit -- any feedback?

Technically, I have already done everything as far as 3DNA v2.0 itself is concerned. What's leftover is distribution, the final stage of a software product, presumably an exciting experience both to the author and the user community. Rutgers has licensed 3DNA and required that it is distributed in a protected fashion, with user registrations etc. In principle, it is easy to release the tarballs of 3DNA v2.0, which I compiled early this year, automatically through a web-form. Even dealing with each individual user's request manually, on a case-by-case basis, should take no longer than a few minutes. Over the times, I have mentioned to Rutgers several times that distributing 3DNA as widely as possible (with proper measure of protection of intellectual property) is to the benefit of everyone who really cares about the software product, and it is also an obligation per the 2008 3DNA Nature Protocols publication.

Xiang-Jun

1493

General discussions (Q&As) / Re: 3DNA version 2.0

« on: July 20, 2009, 07:28:36 pm »

I have registered in 3DNA forum. Would you please give details about downloading 3DNA 2.0 (i read in 3DNA forum that it requires some license, password etc)

Please note that registration with the 3DNA forum is unconnected (at least for the time being) with downloading 3DNA v2.0. I have tried hard to make my point simple and unambiguous, so please follow instructions there.

Xiang-Jun

1494

General discussions (Q&As) / Re: DNA Rotation

« on: July 08, 2009, 11:50:47 pm »

Thanks for using 3DNA. I am glad that you are taking advantage the visualization part of 3DNA: the other day, I blogged on blocview wondering why it has not been used that much.

Could you be more specific? Which command and options did you use? Preferably with a reproducible example?

Xiang-Jun

1495

General discussions (Q&As) / Re: defining a local helix axis

« on: July 08, 2009, 11:15:55 pm »

Thanks for using 3DNA, and posting interesting questions on defining local helix axis and quantifying the kinks in a DNA structure.

3DNA outputs many structural parameters including "Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in the coordinate system of the given structure", and "Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step", as shown in file bdl084.out distributed with 3DNA. In idealized cases, e.g., where a perfectly regular B-DNA fragment connects to a perfectly regular A-DNA fragment, the local helical axis vector should do the trick. However, in normal cases, e.g., for your protein-bound DNA, local distortions make local helical axis associated with each dinucleotide quite irregular (see an worked example below), and as always, one needs to be careful in drawing conclusions from using it.

Local kinks in protein-bound DNAs are normally quantified using roll angle in the literature. See, for examples, the two Chen et al. papers: http://www.ncbi.nlm.nih.gov/pubmed/11724532 and http://www.ncbi.nlm.nih.gov/pubmed/11724533.

Also, you may want to check Curves, which has been used frequently in the literature for quantifying DNA curvature. It is to the users' advantage to have a choice for comparisons before jumping to conclusions. I have tried to build a bridge between 3DNA and Curves to make Curves users' life a bit more straightforward: find_pair have an -c option to generate input to Curves from a PDB file.

Since you are inquiring about "defining a local helix axis", the following message (slightly edited), which I communicated with an acquainted 3DNA user back on January 5, 2007, could be useful and/or more directly relevant.

> [2] my point is that the global axis is NOT displayed in the Raster3D mode.
> Nothing changes when I run frame_mol and then alc2img with the -g option.

[...]That 3DNA forum has been created for general discussions, so that the
community knows that 3DNA is still under active support and further
development.

3DNA certainly has more functionalities than described in our 2003 NAR
paper, and in reality, it is the details that count.

The simplest way to answer your 2nd question is by following an example
such as below:

Code: [Select]

find_pair bdl084.pdb stdout | analyze
rebuild bp_step.par bdl084.alc
rasmol -alchemy bdl084.alc
frame_mol -a -g -m -6,7 ref_frames.dat bdl084.alc bdl084_new.alc
rasmol -alchemy -noconnect bdl084_new.alc
alc2img -a -g -l bdl084_new.alc t.ps
gv t.ps
alc2img -r -a -g -l bdl084_new.alc t.r3d
render < t.r3d > t.avs
display t.avsThe global axis is displayed in t.avs, or t.ps with x-, y- etc labels.

Note: The above "recipe" works with 3DNA v1.5; One should use RasMol 2.6.x, not v2.7.x (a current version of Jmol is also fine) to display ALCHEMY format files properly; The command 'display' is from the ImageMagick package. See 3DNA 2008 NP paper for more examples.
[hr:611u016p][/hr:611u016p]
HTH,

Xiang-Jun

1496

General discussions (Q&As) / Re: Threading DNA

« on: June 22, 2009, 10:17:58 pm »

I wonder if it's possible using 3DNA to superpose a given(input) DNA sequence to the conformation of the DNA in the known protein-DNA complexes from the PDB database.

The short answer is no: 3DNA does not have such functionality built in. However, 3DNA is a tool set that could be used for such purpose. For an example, have a look http://www.ncbi.nlm.nih.gov/pubmed/19289051.

Xiang-Jun

1497

SCHNAaP/SCHNArP / Re: GLH_build() Memory Leak

« on: June 01, 2009, 07:00:27 pm »

I have fixed the memory leak bugs in file rebuild.c. I have also taken this opportunity to tidy up the code base a little bit. Please download the updated version and verify that the bugs are indeed gone.

Thanks,

Xiang-Jun

1498

General discussions (Q&As) / Re: How to make blocview -i work with pymol in batch mode.

« on: May 20, 2009, 07:03:35 pm »

Hi Mauricio,

Thanks for your note. In the current version of v2.0, the system call is as follows:

Code: [Select]

system("pymol -c $pmlfile 2&> x3dna_r3d_pymol.msg");i.e., with the -c option to run pymol in command-line mode. If I remember it correctly, I added this -c option following your suggestion (thanks!),  while you and Guohui helped verifying the recipes for the 2008 3DNA Nature Protocols paper.

I understand what -q means, and could add it to 3DNA v2.0 as you suggested (i.e., -qc). Does it really matter? What differences does it make: -c vs -qc? Could you have a try and report back?

While 3DNA is distributed in binary form for C programs (per Rutgers license policy), the Perl scripts are actually open source. It has been my intention to keep it that way so that users can follow the examples, make changes as needs arise, and create new tools.

Xiang-Jun

1499

General discussions (Q&As) / Please join me in my blog posts!

« on: May 17, 2009, 01:39:42 pm »

I have recently started to blog on topics I am interested in or feel worthwhile to take a note on. The posts necessarily reflect my personal, opinionated views, and you are welcome to make comments.

Xiang-Jun

1500

SCHNAaP/SCHNArP / Re: GLH_build() Memory Leak

« on: May 15, 2009, 11:24:59 pm »

Thanks for reporting the problems you experienced. Could you please be more specific, and better yet, providing me a reproducible example? I will certainly look into it to get it fixed ASAP.

Xiang-Jun