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Messages - xiangjun

Pages: 1 ... 57 58 [59] 60 61 ... 63
1451
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Overall, SCHNAarP was produced 10+ year ago, and it is now superseded by 3DNA (v2.0). That does not mean the underlying algorithms are out of date.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

1452
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

1453
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

1454
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

1455
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

1456
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

1457
General discussions (Q&As) / Re: Base Pair Step Parameters
« on: February 17, 2009, 10:09:53 pm »
Quote from: "rodrigopontiggia"
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

1458
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

1459
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

1460
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.outs
A 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

1461
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]

1462
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

1463
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

1464
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

1465
General discussions (Q&As) / Re: error bars in DNA parameters
« on: December 17, 2008, 09:56:23 pm »
Hi Cathy,

Quote from: "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

1466
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

1467
Quote from: "guohui"
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

1468
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

1469
w3DNA -- web interface to 3DNA / Re: Logo
« on: December 09, 2008, 12:30:12 am »
Hi Guohui,

Good progress!

Try to finish 'fiber' model building first, as suggested earlier. Present the user with a full-list of available models (55), and based on selected model number, ask for sequence or just repeating unit. It is fine to have the most common A-, B-, C- and Z- (not D-, or with D-) form at the top.

I am not a designer either -- in the 3DNA forum, I have been asking for user's contributions. Until very recently have I updated the 3DNA forum logo. But honestly, I do not like the one you currently post there. I have created an alternative as attached here, which has a transparent background.

For 'analyze', you could pre-build all available NDB entries. Thus when a NDB/PDB id is supplied, the results are immediately available.

Keep good work!

Xiang-Jun
[attachment=0:pn02lib2]w3DNA_logo.gif[/attachment:pn02lib2]

1470
General discussions (Q&As) / Re: Continuous polymer
« on: December 03, 2008, 11:05:08 pm »
This is a good question! Unfortunately, 3DNA do not have a direct answer for it (yet). Does anyone know of a general solution to this problem (say, from a commercial or freely available software package)?

In principle, though, one would image to keep each repeating unit (8-bps here) as a rigid body and perform transformations (rotations + translations) to get the next and so on. One way to achieve it is by properly setting coordinate frames.

Xiang-Jun

1471
w3DNA -- web interface to 3DNA / Re: Rebuilding part
« on: December 01, 2008, 01:45:18 pm »
Quote from: "guohui"
For the fiber model-building part, I am trying to use the program "fiber", am I right? This program requires parameter inputs from the screen/keyboard, to provide the sequence information. However, if we want to execute it from the web, this could be a trouble, since we won't be able to type it those information. Is it possible that you can adjust the program a little bit such that all parameters (maybe data files) could be included in just a command line, such as "fiber -s sequence.txt -a fiber_a.pdb"?

Right. User needs to first select a model, which can be provided via a HTML form selection list. Depending on the model selected, the sequence could be fixed, where user just needs to select the number of repeating unit (form input field with type="text"), or user need to input a sequence. The sequence could be from a file which is to be uploaded to the server, or through textarea tag. All such info is collected from a web-based form, and then passed to fiber. The program needs not to be changed, by taking advantage of Unix file indirection, e.g., '<' or '>'. Please play around in command-line first to get it right before you are able to implemented a web-interface to it.

Quote from: "guohui"
Or do you have any other ways to solve this? Can I use "rebuild" function as an alternative? How?

The rebuild program is for a different purpose, thus it is not a substitute for fiber. Let's get fiber functionality done first: itself would be of great value to a large audience.

HTH,

Xiang-Jun

1472
w3DNA -- web interface to 3DNA / Re: What kind of services we will provide?
« on: November 30, 2008, 01:32:06 pm »
      Hi Guohui,

      Good start!

      Overall, I would like to make w3DNA simple, accurate and robust, at least at the very beginning: take, for example, the 'google' home page. Do not put too many stuffs; whatever is there should be useful.

      • Analyzing: list the various 3DNA output files files for download first, followed by any extracted info. A nice, simple add-on would be to mark non-Watson-Crick pairs (or G.U wobble pair).
      • Rebuilding: put fiber model-building part first since this is the most-useful part to the general community; add sequence-specific building funcationality next: do not forget with sugar-phosphate backbone in various conformation, and the simplified Calladine-Drew style in Alchemy format. The download page should also be linked to Jmol/RasMol for online view.
      • Visualizing: blocview is certainly the first choice, followed by stacking diagram, and base-pairing diagram (see the 3DNA NP paper). This is linked directly to the analyzing part.

      You might want to put fiber-model building first in the list, following by visualization. In the home-page, you might also want to put some nice images to illustrate 3DNA major functionality to attract visitors.

      Best regards,

      Xiang-Jun

1473
General discussions (Q&As) / Re: ideal values for the stacking parameters
« on: October 10, 2008, 11:03:10 pm »
Having never performed MD simulations, I am not sure how an idealized uniform structure would effect your comparisons. With 3DNA, you can build a structure with any prescribed step parameters. However, the backbone geometry would normally be distorted, especially at the connections between nucleotides.

What initial structure do you start with for your MD? Can't it be used for your comparison? How about fiber B-form DNA? Any comments from MD experts?

Xiang-Jun

1474
General discussions (Q&As) / Re: Calculating the angle of DNA curvature
« on: September 26, 2008, 11:47:40 pm »
Thanks for reading the 3DNA Nature Protocols 2008 paper (NP2008).

The quota you cited refers to the section titled "Relationship to other programs", more specifically the "-c" option of "find_pair" designed to make Curves users' life a bit more straightforward. Curves is certainly a well-known program in quantifying DNA curvature, as evidenced clearly in literature where DNA bending angles are reported.

In the 3DNA NP2008 paper, protocol (recipe) no. 4 is on "Automatic identification of double-helical regions in a DNA–RNA junction", which provides detailed steps on calculating the angle between helices #1 and #3.  If that's what you want, you may find it worthwhile to (re)read the relevant parts more carefully.

Given the many similar questions recently popped up in the forum, it seems fair to say that quantifying DNA bending angle or curvature is still an open issue,  at least not well-understood by non-experts in the community. From my experience (not just in nucleic acid structures), this is not surprising at all. A seemingly long-solved problem still could bug you down when you try to get to the bottom of it.

HTH,

Xiang-Jun

1475
That's correct.

As a side note, the helical axes in Figure 4 of 3DNA 2003 NAR paper is actually 11 - 1 = 10 fragments which are perfectly aligned in the regular structures.

HTH,

Xiang-Jun

Pages: 1 ... 57 58 [59] 60 61 ... 63

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.