Messages

1526

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

1527

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

1528

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

1529

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]

1530

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

1531

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

1532

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

1533

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

1534

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

1535

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

1536

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

1537

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]

1538

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

1539

w3DNA -- web interface to 3DNA / Re: Rebuilding part

« on: December 01, 2008, 01:45:18 pm »

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.

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

1540

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

1541

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

1542

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

1543

General discussions (Q&As) / Re: local helical parameters interpretation question

« on: September 18, 2008, 12:02:51 am »

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

1544

General discussions (Q&As) / Re: interhelical angles

« on: September 16, 2008, 09:13:47 pm »

Unfortunately, the simple answer is NO.

However, you might want to refer to the 3DNA Nature Protocols paper recipe no. 4 on "Automatic identification of double-helical regions in a DNA–RNA junction" and explanations therein on how this problem is handled in not "a straightforward way" with 3DNA. Browsing the forums should also give your some hints.

HTH,

Xiang-Jun

1545

General discussions (Q&As) / Re: local helical parameters interpretation question

« on: September 16, 2008, 09:05:15 pm »

It is not a surprise to me that the local helical parameters as given in 3DNA could be a bit confusing. I have answered this question several times over the years, mostly before the forum was set up. Excerpted below is one I just dug out:

[1] To refer the orientation and position of one base-pair (bp) relative to
    the other, 6 parameters (3 rotations and 3 translations) are required.
    One set of such parameters is (Shift, Slide, Rise, Tilt, Roll and
    Twist), and the other set is (X-displacement, Y-displacement, Helical
    Rise, Inclination, Tip and Helical Twist).

    Obviously these two sets should be completely reversible/dependent: from
    any one set you can get the other, rigorously. You can verify this point
    using "step_hel", a utility program in 3DNA. Graphically this is best
    illustrated by the Calladine-Drew A to B transition model by introducing
    uniform Roll and Slide values at each dinucleotide step. You could see
    these images in 3DNA website, Examples/Calladine_Drew/ directory in 3DNA
    distribution and 3DNA user's manual. The key point is that by
    introducing Roll, you also get Inclination, and with Slide, you get
    X-displacement.

    The "rebuild" program in 3DNA can construct a DNA structure using either
    set of these parameters. Examples of such input files (e.g.,
    "bp_step.par" and "bp_helical.par") can be generated by
    "analyze". Please have a look of the Examples/Analyze_Rebuild directory.

[2] The define a local helical axis, we need two base-pair reference
    frames (i and i + 1). 3DNA finds the single-helical axis (which is
    actually dx times dy) that brings i to coincide with i + 1 by a Helical
    Twist angle. The position which this helix passes through is defined by
    Chasles' theorem as detailed in Figures 12 & 13 of Backcok et al.
    (J. Mol. Biol. 1994, 237, pp 125-156). The calculation of
    X-displacement, Y-displacement, Tip and Inclination is then exactly as
    described in SCHNAaP (J. Mol. Biol. 273, 668-680, i.e., 3DNA calculates
    a set of local helical parameters instead of linear global ones as given
    in SCHNAaP and NewHelix/FreeHelix.)

    To make the above point clear, let's use A1-A2-A3 triplet as an example.
    First, A1-A2 define a local helical axis and a set of local base-pair
    helical parameters are calculated. In 3DNA, these parameters are defined
    in a symmetric manner that bp A1:T1 and bp A2:T2 have exactly the same
    values except for a sign reversal for Y-displacement and Tip.
    Similarly, step A2-A3 define another set of local base-pair helical
    parameters. Thus bp A2:T2 has two sets of helical parameters associated
    with it depending on its context, i.e., either with bp A1:T1 or with bp
    A3:T3. Moreover, the local helical rise and helical twist are directly
    related to a dinucleotide step. These are the reasons that "Local
    base-pair helical parameters" as given in 3DNA refer to base-pair steps.

Please also refer to another post in this forum on "h-twist vs. twist" and the link therein.

HTH,

Xiang-Jun

1546

General discussions (Q&As) / Re: interpretation of output file

« on: September 13, 2008, 05:18:27 pm »

Again, as recommended clearly in the guideline, please provide a minimal, reproducible example to help others HELP YOU.

on your site there is only one instruction how to do find_pair, so I can run only this command.

As the author of "find_pair", I know clearly that it does not produce output on "deviation of the global helical axis from a regular linear axis".

I am certainly not in a position to answer the reviewer's questions to your paper. As a general rule, it is dangerous to use something you do not understand. You should clarify the issues beforehand instead of afterwards.

Overall, if you do not know how to use "fiber" to build fiber models,  not being able to find and follow the instructions in the 3DNA users' manual, clearly 3DNA is not the right tool for you. Curves is an excellent alternative and it is widely used to quantify DNA curvatures.

Good luck!

Xiang-Jun

1547

General discussions (Q&As) / Re: interpretation of output file

« on: September 10, 2008, 10:04:03 pm »

Well, I do not intend to be mean, but have you ever thought of answering the requests/questions in my reply to your initial post? Going through those questions would have clarified your understanding of the issues and helped other 3DNA users as well.

It might help to (re)read the post "Welcome message from Xiang-Jun Lu", and follow the link on "How To Ask Questions The Smart Way?"

Best regards,

Xiang-Jun

1548

General discussions (Q&As) / Re: interpretation of output file

« on: August 11, 2008, 09:56:53 pm »

Could you please tell me "Deviation from regular linear helix: 3.32 (0.37)".
Is it in angstroms or degrees? Is it a big bend or a mild one?

It is in angstroms. Based purely on the number, I would guess it is a mild one. As always, however, a number is just a number, and you should use a visualization tool (e.g., RasMol) to see/judge for yourself.

Is it possible to see "normal" DNA parameters to compare with the results from the output file? Which parameters other than the "Deviation from regular linear helix" indicate if the bend is big or mild?

Try use the "fiber" program to build regular B- and A-DNA models and analyze them. What would you get? Check and compare them with the examples directory (analysis/rebuilding) of A-, B- and nucleosome DNA structures adh006/bdl084/pd0001. It would be helpful that you summarize and post back a table of your findings.

In our structure, a protein interacts only with the half of the double-stranded B-DNA. How can I determine that only one half is bent?

3DNA works on a user-specified PDB file, which could be the whole structure or half of it.

HTH,

Xiang-Jun

1549

General discussions (Q&As) / Re: Rebuilding protonated RNAs with non-canonical basepairs

« on: July 30, 2008, 11:25:21 pm »

Sorry, I mis-formulated... I meant:
I can rebuild a U-U basepair, but analyzing does not work.

Well, it is not a problem of the 'analyze' program either. As a side note, how many such misunderstandings exist in literature?

Check FAQ #6 carefully: you should be able to get the answer. For your own understanding of the issue and to the benefit of other users, I am hoping that you would summarize your solution and post it back   . Otherwise, I will have no incentives on follow-up questions    

HTH,

Xiang-Jun

1550

General discussions (Q&As) / Re: calculate step parameters of a funny step

« on: July 23, 2008, 10:34:44 pm »

Read the FAQ #6. Specifically, check file 'misc_3dna.par': one of the geometric constraints is the angle between base normals, with a default of 65 degrees. The base pair 58 (58 G and 233 C) you referred to could be larger than it.

As suggested in previous forum posts, you can always manually edit the 'find_pair' output before feeding it into 'analyze' to get the parameters of arbitrary bps or steps you are interested in.

HTH,

Xiang-Jun