Messages

1501

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

1502

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

1503

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

1504

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

1505

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

1506

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?"

1507

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

1508

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

1509

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.

1510

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

1511

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

1512

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

1513

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

1514

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

1515

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

1516

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

1517

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

1518

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

1519

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

1520

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

1521

General discussions (Q&As) / Re: Noobie question on building triplex DNA

« on: April 30, 2009, 10:50:49 pm »

Sorry for the noobie question, but is it possible to build a triplex DNA from scratch? If not, is it possible to take a .pdb file of a triplex DNA and mutate it to my own sequence? This would involve insertion of an extra residue in the loop region. I would later like to save the new coordinates in .pdb format for molecular dynamics studies.

This is good question: it clearly illustrates the need for a tool to manipulate/build/edit nucleic acid structures in 3-dimensional space. Ideally, it would be with an interactive GUI. Aren't there tools already available, commercial or free, that fit the bill?

As far as 3DNA goes, some of its 55 fiber models are triplexes. Starting from a PDB file of a triplex DNA and then mutating it to your specific sequence, or inserting an extra residue in the loop region,  are doable with 3DNA, along the same line as shown the thread "mutating DNA in DNA protein complex". Of course, the operations are not automated -- tedious and error-prone: you've got to know exactly what you want to do, and better have some programming skills to perform necessary geometric transformations.

Overall, 3DNA can do a lot, but there are many more things that can not be done easily or at all. It is a long journey from SCHNAaP/SCHNArP to 3DNA, and I have felt strongly for quite some time the need to move forward -- based on my 10+ years experience in creating and supporting SCHNAaP/SCHNArP/3DNA,  I have been building a new set of tools that can better meet the challenge of structure explosions. Among its many possible functionalities, it would make some of the requests in the forum, including this one, possible or much easier.

HTH,

Xiang-Jun

1522

General discussions (Q&As) / Re: how to minimize DNA built with fiber?

« on: April 22, 2009, 11:49:17 pm »

Could you be more specific? Which model did you use, and what's the sequence? The fiber models from 3DNA should have standard geometry and proper linkage. I am wondering how it could have broken bonds.

Xiang-Jun

1523

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

« on: April 20, 2009, 11:33:53 pm »

Dear Ramon,

Thanks for bringing up the issue of downloading 3DNA v2.0. Dr. Olson is the proper contact for further instructions. Rutgers has imposed some licensing policy that is beyond my interest to get a hand on. Here is an excerpt, verbatim, of the message I sent to Dr. Olson regarding the release of 3DNA v2.0, after I uploaded the distribution tarball files for the most common operating systems (that I have access to) to the server in a password protected directory:

It is quite a while since our 3DNA NP paper was published. Over the
time I have received a couple of requests to download 3DNA v2.0
mentioned in our paper. Due to (complicated) license issues, I think
you are in a position to handle this issue. By getting more directly
involved, you would understand better what it means to maintain and
support a software.

As far as what's new with v2.0, it has already been mentioned in http://3dna.rutgers.edu/. To recap, v1.5 as currently available in http://rutchem.rutgers.edu/~xiangjun/3DNA/download.html was compiled 6 years ago that had never been updated. Of course, it still serves the majority of common cases very well, and I have used it as a test case of how robust my original implementation is (which is quite assuring, BTW). Of course, over the years, I have fixed bugs, added new features, and updated 3DNA to handle the remediated PDB files etc, which I have communicated with users on a case-by-case basis. The v2.0 contains an accumulation of all these refinements. More importantly, in writing the 3DNA Nature Protocols paper, I have added more command line options, new scripts and worked examples (NP_Recipes.tar.gz). Accurately reproducing these examples and understanding how each works, users would see why 3DNA is called 'a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures' . Aren't these sufficient reasons to upgrade?

Xiang-Jun

1524

General discussions (Q&As) / Re: how the cartesian coordinates transform to PDB format

« on: April 20, 2009, 11:14:46 pm »

First, thanks to Ramon for getting actively involved in answering other user's question. Over the years, it is my hope that 3DNA forum could turn into a virtual community where more people would participate in discussing issues related to nucleic acid structures. I am hoping others will follow your lead, and the 3DNA forum becomes more active.

Now to Si-Ya's question. 3DNA starts from a nucleic-acid containing structure in PDB format. Note specifically the coordinate section. As a more concrete example, have a look of the residue DT8 in chain A of entry 355d, as shown below:

Code: [Select]

ATOM    142  P    DT A   8       5.196  18.285   8.120  1.00 13.16           P 
ATOM    143  OP1  DT A   8       3.928  18.831   8.653  1.00 14.21           O 
ATOM    144  OP2  DT A   8       5.211  16.970   7.475  1.00 12.40           O 
ATOM    145  O5'  DT A   8       5.818  19.323   7.094  1.00 12.21           O 
ATOM    146  C5'  DT A   8       6.104  20.657   7.510  1.00 10.87           C 
ATOM    147  C4'  DT A   8       6.937  21.347   6.466  1.00  9.09           C 
ATOM    148  O4'  DT A   8       8.271  20.815   6.382  1.00  8.32           O 
ATOM    149  C3'  DT A   8       6.372  21.324   5.049  1.00  9.83           C 
ATOM    150  O3'  DT A   8       6.060  22.664   4.718  1.00 11.88           O 
ATOM    151  C2'  DT A   8       7.476  20.700   4.203  1.00  8.59           C 
ATOM    152  C1'  DT A   8       8.709  20.942   5.040  1.00  7.33           C 
ATOM    153  N1   DT A   8       9.786  19.985   4.858  1.00  7.74           N 
ATOM    154  C2   DT A   8      11.028  20.464   4.498  1.00  6.25           C 
ATOM    155  O2   DT A   8      11.253  21.654   4.285  1.00  7.74           O 
ATOM    156  N3   DT A   8      12.003  19.496   4.402  1.00  6.29           N 
ATOM    157  C4   DT A   8      11.852  18.139   4.631  1.00  5.16           C 
ATOM    158  O4   DT A   8      12.819  17.406   4.547  1.00  6.98           O 
ATOM    159  C5   DT A   8      10.502  17.708   4.979  1.00  5.39           C 
ATOM    160  C7   DT A   8      10.230  16.254   5.214  1.00  6.78           C 
ATOM    161  C6   DT A   8       9.556  18.638   5.074  1.00  5.19           C 
It is not just about the coordinates, but also about the naming convention of the base and backbone atoms. For example, for thymine, you have N1--C2--N3--C4--C5--C6 ring atoms, and O2 and O4 atoms attaching to C2 and C4.

As your example shows, it is clearly not in proper PDB format. It seems to be in xyz format. One might consider using 'babel' to convert it into PDB format. However, this converted version is not the one accepted by 3DNA, for reasons detailed in the above paragraph. I vaguely remember there is some tool to do proper conversion to PDB with correct atom names. Google it to see for yourself. For your specific purpose, I guess the 'simplest' way is to write a script to perform the conversion by taking into atom name convention into consideration.

HTH,

Xiang-Jun

1525

General discussions (Q&As) / Re: Find DNA-protien contacts using 3DNA

« on: April 18, 2009, 01:45:09 pm »

Is there a direct option/function to find amino acid atoms around base pairs, i.e. protein contacts with DNA/RNA? Or can you suggest a way to combine various 3DNA functions to approach this?

No, there is no such as an option in 3DNA to find contacts of amino-acids with nucleotides, as the "-w" option for waters.

In the same paper, I also mentioned:

The interactions with users from different backgrounds have given us the incentive to adapt the programs for further applications in related fields, for example, RNA structure-motif identification and alignment, structural analysis of DNA–protein complexes and modeling RNA folds. The reference-frame-based description of three-dimensional spatial geometry makes the methodology and algorithms in 3DNA directly applicable to these problems and treats them in a rigorous and consistent fashion

Specifically, for one of my current research projects, I have written a program named SNAP (Structure of Nucleic Acids and Protein) which has this functionality, among other things. However, SNAP is not part of 3DNA: I am currently beginning to write a manuscript on this topic, and will make it available in due time.

Of course, if you check the literature, there are many ways to find the contacts between aa with nt: e.g., Kono/Sarai, Pabo + Siggers/Honig, and Luscombe/Thornton.

Xiang-Jun

[hr:1je7sv3u][/hr:1je7sv3u]
PS. As a side note, in 3DNA Nucleic Acids Research, 2003 (Vol. 31, No. 17, 5108--5121), I mentioned the following:

Since the six base pair parameters uniquely define the relative position and orientation of two bases, they can be used to reconstruct the base pair. Moreover, the parameters provide a simple mechanism for classification of structures (55) and database searching (X.-J. Lu, Y. Xin and W.K. Olson, unpublished data).