Messages

1501

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

1502

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

1503

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

1504

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

1505

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).

1506

General discussions (Q&As) / Re: Calculation of Jtwist, Jroll and Jslide for junctions

« on: April 01, 2009, 09:07:51 pm »

Thanks for the reference. While 3DNA is not directly applicable for calculating such parameters, it could help in some ways, e.g., to identify the double helical regions and get the helical axes etc.

Of course, you could always check with the original authors for further technical details (e.g., the program to reproduce their results). If you want to implement their method yourself and would like to share, I am willing to help in a sensible way.

Xiang-Jun

1507

General discussions (Q&As) / Re: Calculation of Jtwist, Jroll and Jslide for junctions

« on: March 31, 2009, 11:25:50 pm »

How to calculate Jtwist, Jslide and Jroll using 3DNA software for junction structure?

I am not familiar with the names Jtwist, Jslide and Jroll, and they are not calculated by 3DNA.

Would you mind sharing more details, e.g., providing a reference?

Xiang-Jun

1508

SCHNAaP/SCHNArP / Re: SCHNArP: Global Parameters

« on: March 20, 2009, 10:58:05 pm »

Well, once you try to get into details on how things actually work in SCHNAarP, or any software tools in that matter,  you will surely have lots of questions. Getting the software compiled and run is just the beginning.

Overall, SCHNAarP was produced 10+ year ago, and it is now superseded by 3DNA (v2.0). That does not mean the underlying algorithms are out of date. Just on the contrary, the mathematics is valid and solid, and it forms one of the foundations of 3DNA. Yet by design, the reference frames in CEHS and SCHNAaP only apply to double helical DNA/RNA structures (with Waton-Crick bps). As a special note, stretch for a Watson-Crick base-pair is ~5.4 A instead of 0 A, as would be expected, and from other analysis programs.

Now for your specific questions:

There is no special documentation to the file format on Sequence-GLH parameter file. It would be self-explanatory by following an example. For your case, first enter #2 for "Use GLOBAL helical parameters." Then I enter #1 for "Uniform regular helix" and you will get an output file "GLH_seq.dat". Examine it and post back here what you find. And have a look of 1bna.glh following schnaap.

Building RNA structure from a set of SCHNAaP global parameters would be practically meaningless (see above). With the source code in hand and once you get to the bottom of it, you could borrow the idea to apply to your specific applications. This does take time and efforts -- it is not just about the C code, but more about the underlying mathematics and the nucleic acid structure problems being addressed.

HTH,

Xiang-Jun

1509

SCHNAaP/SCHNArP / Re: SCHNArP/SCHNAaP c source code

« on: March 18, 2009, 11:59:27 pm »

All bug fixes / changes have been incorporated into the code base from the download site. Thanks to 'clarebonk' for reporting and testing!

As always, bug reports and comments are gratefully received.

Xiang-Jun

1510

SCHNAaP/SCHNArP / Re: SCHNArP/SCHNAaP c source code

« on: March 17, 2009, 10:18:33 pm »

Very strange. It should work -:)

What OS and compiler are you using? Is it 'gcc'? Did you change all four NR functions? For verification purpose, please send me your finished 'cmn_fncs.c' file by email.

Xiang-Jun

1511

General discussions (Q&As) / Re: Building a DNA superhelix

« on: March 04, 2009, 11:16:35 pm »

Thanks for the info. Just to be precise, the link you gave is broken: it should also include the ending characters in the URL. For the benefit of other viewers, here is the correct one with title of the paper as link text: Geometry of the Nucleosomal DNA Superhelix by Thomas C. Bishop. (We all make simple mistakes, and I hope you won't mind my pointing your minor typo out  :roll:. I am hoping you and others will do the same to any 3DNA-related issues. Every bug report or correction etc would be gratefully received!

I have no problem in accessing this paper. I think it is a nice piece of work. It is actually in the 3DNA citation list. I should have read the abstract before, but did not get into the main text. To be realistic, though, I do not think I have that much spare time right now to understand and implement the algorithm to fit your purpose -- it won't be a trivial take, especially to get it done efficiently and robustly. You could contact the author directly for further details. Maybe we could make an arrangement to incorporate Dr. Bishop's method into 3DNA (with proper attributions, of course).

Thanks for your cooperation, and hopefully more 3DNA users would follow your example.

Xiang-Jun

1512

General discussions (Q&As) / Re: Building a DNA superhelix

« on: March 03, 2009, 11:46:11 pm »

Dear Miguel,

Thanks for posting your DNA super-helix building question here. Currently, 3DNA does not yet have the functionality. As you noticed, Arvind posted a related question, i.e., analyzing a DNA super-helix to give its pitch and radius.

Essentially, this is the same issue looked from different perspectives, in a sense similar to SCHNAaP/SCHNArP and analyze/rebuild for DNA/RNA duplex. Any rigorous treatment should be mathematically reversible, i.e., given a super-helix, one can derive a set of pitch/radius parameters; conversely, from this same set of parameters, the original super-helix should be rebuilt without loss of information. I would like to hear more on related issues in the literature. Any clues?

Xiang-Jun

1513

General discussions (Q&As) / Re: Base Pair Step Parameters

« on: February 21, 2009, 01:05:55 pm »

Hi Rodrigo,

Your case is yet another example of the importance to be specific when asking questions and in discussions.

From your attached 3DNA output file, the H-bonds are normal for what would be expected for Watson-Crick pairs:

Code: [Select]

****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
   1 G-----C  [3]  O6 - N4  2.86  N1 - N3  2.90  N2 - O2  2.81
   2 A-----U  [2]  N6 - O4  3.03  N1 - N3  2.90
   3 A-----U  [2]  N6 - O4  2.98  N1 - N3  2.91
   4 A-----U  [2]  N6 - O4  2.94  N1 - N3  2.95
   5 A-----U  [2]  N6 - O4  2.89  N1 - N3  2.96
   6 G-----C  [3]  O6 - N4  2.95  N1 - N3  2.93  N2 - O2  2.85
   7 A-----U  [2]  N6 - O4  3.05  N1 - N3  2.92
   8 A-----U  [2]  N6 - O4  3.03  N1 - N3  2.94
   9 A-----U  [2]  N6 - O4  2.96  N1 - N3  2.92
  10 G-----C  [3]  O6 - N4  2.91  N1 - N3  2.91  N2 - O2  2.80
  11 A-----U  [2]  N6 - O4  3.00  N1 - N3  2.89
  12 A-----U  [2]  N6 - O4  2.95  N1 - N3  2.96
****************************************************************************

Naturally, the six base-pair parameters have mean and std values in ranges reported in the literature:

Code: [Select]

****************************************************************************
Local base-pair parameters
     bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening
    1 G-C      -0.23     -0.18     -0.63    -20.29     -2.28     -0.66
    2 A-U       0.09     -0.04     -0.48    -13.64    -10.06      4.26
    3 A-U       0.06     -0.06     -0.53    -11.24    -12.42      2.82
    4 A-U       0.09     -0.03     -0.62    -13.46    -13.99      0.86
    5 A-U       0.18      0.01     -0.56    -15.56    -12.75     -1.66
    6 G-C      -0.05     -0.03     -0.69    -25.26    -19.76      2.36
    7 A-U       0.06      0.01     -0.35     -7.49     -7.94      4.36
    8 A-U       0.14     -0.00     -0.49     -8.36    -11.15      3.57
    9 A-U       0.09     -0.04     -0.34     -6.42    -10.45      1.32
   10 G-C      -0.11     -0.13     -0.33     -9.45    -12.75      1.08
   11 A-U       0.08     -0.08     -0.36     -9.60    -12.41      3.48
   12 A-U       0.16     -0.09     -0.35     -1.29    -11.67      0.95
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      ave.      0.05     -0.06     -0.48    -11.84    -11.47      1.89
      s.d.      0.12      0.06      0.13      6.42      4.05      1.91
****************************************************************************
Thus, from what I have in hand, nothing appears (to me) really unusual here. Of course, it would also be helpful to analyze your structure with other programs, e.g., Curves, to see what you get.

HTH,

Xiang-Jun

1514

General discussions (Q&As) / Re: Base Pair Step Parameters

« on: February 17, 2009, 10:09:53 pm »

I´m analyzing an double helix RNA with a modified nucleotide. The effect of the modification pushes one of the bases but doesnt affect complementary one. stragger, proppeler and Buckle are very affected. Since it affects only one base of the base pair I dont know if it is correct two analyze roll and tilt. May be its a wrong average of a non-averageble structure.

Again, it would make life easier for me and other viewers of this forum to understand exactly what you mean if you have provided more details,  i. e., the PDB file containing the fragment you are having trouble with and corresponding 3DNA output. Remember to help as much as possible to others so they can help you!

In a general sense, I believe I know what you mean, and I am glad that you bring up this issue. There is still confusions in the literature regarding analysis of non-Watson-Crick base-pairs and their associated helical regions, which are prevalent in RNA structures. Without going into specific details, I would suggest that you leave out each such pair and its two associated steps from averaging with other normal WC pairs/steps. A comparison is meaningful only if its parts are comparable, which is not the case for a WC vs non-WC pairs.

However, such non-WC pairs should not be ignored  -- instead, they should be treated separately and with more care. 3DNA can help in pursuing such cases further, especially in the context of the structural database (NDB/PDB), with its various visualization and analysis tools.

HTH,

Xiang-Jun

1515

General discussions (Q&As) / Re: stability of rna structure

« on: February 11, 2009, 08:39:27 pm »

Hi,

You have an interesting RNA structure. In agreement with you, I do not think that you can pick up "the best based on structural parameters alone". In addition to "give odd values" of the structural parameters, what would be your reference for your comparison? 3DNA does not fit the bill here. Maybe you could get more helpful feedbacks from mailing lists such as GROMACS, AMBER etc packages.

From a pure structural point of view, given a cluster of similar structures, one could perform all-vs-all RMSD fitting to find the "centroid" (i.e., the one with minimum overall RMSD against others) as a representative.

HTH,

Xiang-Jun

1516

General discussions (Q&As) / Re: unknown step values

« on: February 05, 2009, 12:48:48 am »

Things would have been much clearer if you have provided a reproducible example, as requested.

Lacking that info, I would guess there are some missing bps as identified directly by 'find_pair'.

You might also try '-c' option with 'analyze'.

HTH,

Xiang-Jun

1517

w3DNA -- web interface to 3DNA / Re: analysis outputs

« on: December 28, 2008, 10:30:15 pm »

Hi Guohui,

Code: [Select]

1WD1.inp auxiliary.par bp_order.dat col_chains.scr hstacking.pdb
1WD1.out bestpairs.pdb bp_step.par col_helices.scr ref_frames.dat
1WD1.pdb bp_helical.par cf_7methods.par hel_regions.pdb stacking.pdb
1WD1.outsA brief description of nine relevant files for double helical structure analysis is at URL: http://rutchem.rutgers.edu/~xiangjun/3DNA/examples.html

You do/should not need to put too much information in w3DNA -- that would cause more confusions than clarify issues. There are many auxiliary files generated with 3DNA, depending on which program or option is used. In my experience, I have not received that many questions regarding the various non-out files. For simplicity, only the .out file should be linked, at least at this stage. Key parameters are presented in tables, as you have already done.

Given below is a brief description of the files in your list, but not mentioned in the 3DNA examples link:
[ol:19tgzkup][li:19tgzkup]bp_order.dat -- an intermediate file related to base-pair and helical region finding algorithm.[/li:19tgzkup]
[li:19tgzkup]chains.scr -- rasmol script to color each chain separately.[/li:19tgzkup]
[li:19tgzkup]bestpairs.pdb -- multiple base-pairs coordinates in PDB format, each expressed in its reference frame, as identified in double helical regions; corresponding to bps in the .inp file from 'find_pair'.[/li:19tgzkup]
[li:19tgzkup]col_helices.scr -- rasmol script to color each helical region separately.[/li:19tgzkup]
[li:19tgzkup]hel_regions.pdb -- multiple helical regions in PDB format, as identified by 'find_pair'.[/li:19tgzkup]
[li:19tgzkup]1WD1.outs -- similar to .out file, but corresponding to 'find_pair -s' option. As we discussed before, we should always run 'find_pair -s ... | analyze' to collect backbone torsion angles and sugar conformational parameters in tables.[/li:19tgzkup][/ol:19tgzkup]

For w3DNA, the major focus should be a robust and efficient web-interface to commonly used 3DNA functionality, targeted at the general audience. There are so many technical details that are hard to explain to non-experts, to some extent, even to the experts in nucleic acid structures. Along this line, I feel it would be helpful to separate 'Fiber model' as a main category and set it as default of w3DNA.

HTH,

Xiang-Jun

1518

w3DNA -- web interface to 3DNA / Re: baselist

« on: December 23, 2008, 11:02:12 pm »

Hi Guohui,

The way you suggested might work most of the time, but it is not a general approach. Certainly one should not count on the naming convention of the nucleotide residues to judge its identity. On the other hand, it really does not matter (that much) which modified base you use -- a generalized Atomic_N|n.pdb will do.

I could have automated this process by default, but decided to leave it as is. I have an updated version of 'baselist.dat' and 'atomlist.dat' that works for the latest NDB (Dec. 19, 2008 release), and I have attached them with this post. In general, you could write a script that process each NDB entry with 'find_pair -s' which should identify each unknown nucleotides. You could then update your list accordingly.

I have refined 3DNA v2.0, especially with regard to the NP_Recipes/ directory, a few months back. The ones intended for "official" release are currently at http://3dna.rutgers.edu:8080/3DNA_v2.0/. The directory is password protected: v2_beta/qB78Yaz. Please use this version to replace to one you are using.

HTH,

Xiang-Jun[attachment=1:3jea5n73]baselist.dat[/attachment:3jea5n73]

1519

w3DNA -- web interface to 3DNA / Re: NMR analysis

« on: December 23, 2008, 10:41:56 pm »

Code: Text

1. Now, I assume that bases are in the same order in both files of 1KX5.inps and bp_step.par. What I mean here is, the first base in the bp_step.par is the first base listed in the 1KX5.inps, second to second, and so on. By presenting the base step parameters I would need to tell users the associating chain and residue information of each base.

With "find_pair -s" option, and "analyze", you will get an output file with ".outs" extension It contains all information necessary to local each residue unambiguously -- see the section "RMSD of the bases". The newly added Perl script 'expand_ids' in v2.0 does this.

Regarding analysis of NMR structures, I do not think there is a fixed number of models in the ensemble]representative[/i] NMR structure. Use "ex_str -h" to extract it.

Xiang-Jun

1520

w3DNA -- web interface to 3DNA / Re: w3dna web progress

« on: December 22, 2008, 10:04:24 pm »

Hi Guohui,

The new site is really shaping up, especially 'blocview' is working -- which means the web-environment is set up correctly now.

At this stage, I think you could focus on getting fundamentals done, leaving the fancy parts later. Some random thoughts:

• Put site logo at the top-left, with text in the right
• Possible title text could be: w3DNA -- a web-interface to (commonly used functionality of?) the 3DNA software package for (the analysis, rebuilding and visualization of?) three-dimensional nucleic acid structures
• Give the three sections "Analysis" ... a different font/size; using style-sheet to get rid of the link-underline
• In fiber models section, I do not think we should provide "Mixing form (A, B, C, Z)": this is a section for (experimental) fiber-based models ONLY.
• Again, in fiber models section, make the selection list more specific and informative by providing more information regarding each model, instead of the generic "Model-xx form fiber". Run 'fiber -m' to see the detailed info.

That's it for now, more to follow later on.

Xiang-Jun

1521

w3DNA -- web interface to 3DNA / Re: Logo

« on: December 22, 2008, 09:42:16 pm »

Hi Guohui,

Regarding the mini-version of the logo, you can simply use gimp or any other image processing tools to resize it. As I said before, I am really not an artist at all. The logo I gave you was produced with a web-based logo generator so take it as a placeholder: there is certainly better ways to get it done.

Xiang-Jun

1522

General discussions (Q&As) / Re: error bars in DNA parameters

« on: December 17, 2008, 09:56:23 pm »

Hi Cathy,

Can you advise the best way to determine or estimate error in parameters such as slide, twist, roll, x-displacement for a given estimated coordinate error? (in our case refinement programs indicate the coordinate error is ~0.3 Angstroms).

All the nucleic acid analysis programs I know of, 3DNA included, calculates a set of structure parameters (slide, roll etc) based on given x-, y- and z-coordinates in PDB format and the coordinate uncertainty (B-factor) is not taken into account.

In NMR derived structures, one has an ensemble of models that fit the constraints, and analyzing all of them would give a mean/std of the structural parameters. It seems there is only one model in x-ray determined structures, and I do not know how the coordinate error in x-ray crystal structures can be directly applied to estimate errors in parameters. I would imagine that the errors in structure parameters should be relatively insensitive to coordinate error: the parameters are based on base-pair plane(s), averaged over all the base atoms whose uncertainty could conceal out.

Hope this helps a little bit: sorry for not being able to provide a more direct answer. Wilma could provide you with more insights into this issue.

Xiang-Jun

1523

w3DNA -- web interface to 3DNA / Re: web access

« on: December 12, 2008, 09:46:15 pm »

Hi Guohui,

It certainly should not be that hard. The system administrator should be able to set up the X3DNA environment variable and add $X3DNA/bin directory to command line search path, so the 'apache' process, or all users, can access them.

This is clearly an IT issue where Wilma should be able to play a crucial here. In the lab I am working, there is a (part-time) system-admin to solve such issues.

While the problem persists, you could focus on the rebuilding and analysis parts to get them done in a more decent form. As for 'blocview', the system needs to have MolScript, Raster3D, and ImageMagick installed, and properly configured for system-wide access. You could (through Wilma, perhaps) check with the NDB/PDB people -- they use 'blocview' for all the nucleic-acid containing structures.

Have a good weekend.

Xiangjun

1524

w3DNA -- web interface to 3DNA / Re: Jmol as an alternative for visualization?

« on: December 09, 2008, 04:57:14 pm »

Regarding to the fiber model construction, Wilma suggested generate a fiber with combination of different fiber models, such as 5 repeats A form + 5 repeats B form. We understand that the difficulty is the connection of two fiber models (backbones). What do you think of having this option on our web server?

I understand Wilma's point, but I honestly do not think it is a good idea here. There are could possibly be many different combinations of the various fiber models, which could be very creative, but  arbitrary. This is exactly what I want to avoid in this work, but it could possibly be left to another paper.

Basically, this is not a scientific paper, but a web-interface to commonly used functionality in 3DNA, and we've already had many stuffs to offer. Additionally, as a general design principle, the web-interface should be simple, targeting the non-expert users. Power-users will play directly with the command-line version.

Xiang-Jun

1525

w3DNA -- web interface to 3DNA / Jmol as an alternative for visualization?

« on: December 09, 2008, 02:35:29 pm »

Hi Guohui,

I noticed that you are using WebMol for visualization, which is fine. However, you might consider to add Jmol as an alternative, at least. Jmol seems to be quite popular right now with an active community. I have recently asked a question regarding Jmol support on alchemy file format there, and received near ten responses.

Also, for the fiber models, I thought we could have a page with all 55 models each with images in (three) different views, citations to the original references etc. This will give users a direct impression on the comprehensiveness of possibilities available with w3DNA/3DNA. We certainly have no matches, as far as I am aware of. A handy (robust and efficient) fiber-model generation and visualization service will by itself be a useful tool to community at large (e.g., for educational purpose), as I mentioned to you before.

Thanks for answer questions in the open 3DNA forum. You will realize that it is good thing to do: just keep doing it!

Xiang-Jun