Messages

1141

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

« on: July 23, 2008, 10:27:15 pm »

There is nothing special about U-U pair in rebuilding. Could you please provide a minimal reproducible example? You could take advantage of the attachment functionality.

Xiang-Jun

1142

General discussions (Q&As) / Re: Multiple global helical axes in one structure, how to calc?

« on: June 25, 2008, 09:55:59 pm »

This question deserves as a FAQ now. Indeed, in the coming 3DNA Nature Protocols paper (anytime soon!), there is an example which involves quantifying the bending angle between two relatively straight helix regions in a DNA-RNA junction structure.

To answer your question now, yes, you need to analyze the two helical regions separately to get the helical axis vector for each, and then to calculate the angle between them. The "analyze" program always takes each structure fed to it as a whole, and outputs a ls-fitted global linear axis if the structure overall does not deviate significantly from a regular helix.

You might also want to play with Curves, which outputs a bending angle as part of its global analysis. As you know, this method is quite frequently mentioned in the literature.

HTH,

Xiang-Jun

1143

General discussions (Q&As) / Re: rotate_mol rotfile.dat

« on: June 11, 2008, 07:47:19 pm »

The format of the transformation matrix expected by 'rotate_mol' should be as follow:

Code: [Select]

   1  # x-, y-, z-axes row-rise
      0.0000      0.0000      0.0000
      0.3654     -0.9308      0.0000
     -0.1924     -0.0755     -0.9784
      0.9107      0.3575     -0.2067
It needs to be fed with option "-t=rotmat.dat": there is a typo in the help message, which has been fixed in v2.0. i.e.,

Code: [Select]

rotate_mol -t=rotmat.dat sample.pdb sample_rmat.pdbIn the coming 3DNA Nature Protocols paper, we have a concrete example of this functionality used to set an DNA-RNA junction structure with one helix region along x-axis, another (decomposed orthogonal component) along y-axis.

HTH,

Xiang-Jun

1144

Related topics / Re: What other software is available?

« on: May 06, 2008, 11:02:29 pm »

Thank for posting a 3DNA-related question in the forum. I am hoping more people would share their experiences to questions like this one.

Depending what you want to do, you might check NAB from David Case's group.

HTH,

Xiang-Jun

PS: It helps to provide a link when referring to a resource, e.g. model.it.

1145

General discussions (Q&As) / Re: Dealing with DNA-Protein complexes

« on: May 06, 2008, 10:40:31 pm »

Thanks for posting your step-by-step procedures: now the issue becomes quite clear.

But, as you said, both structures are using the 1st base-pair reference frame. In the case that the DNA structure is bent (like in 1BDT) using the 1st base-pair reference frame is an issue as the DNA structure is overlapping the protein structure. That is why I was asking if one could set another base-pair as reference frame.

So the answer to your question is yes: you can set with reference to any bp-frame within the structure just by setting the option such as -6 for the 6th bp. When given two numbers, such as -6,7, the middle frame of bp step 6-7 is used to the orient the structure.
[hr:2fhadkdj][/hr:2fhadkdj]
If you ran "frame_mol -h", you will see:

Code: [Select]

-n1[,n2] base-pair serial number(s) [no spaces around ,]and in the example session,

Code: [Select]

EXAMPLES
        To set the Dickerson-Drew dodecamer CGCGAATTCGCG duplex structure
        (bdl084.pdb) with its minor groove at the middle A6-T7 step facing
        the viewer:
            find_pair bdl084.pdb stdout | analyze
            frame_mol -m -6,7 ref_frames.dat bdl084.pdb bdl084_new.pdb
        Check Examples/Calladine_Drew/ subdirectory for more examples
As I mentioned in my response to your first initial post, in modeling DNA structure from a DNA-protein complex, you could divide the DNA structures into fragments: vary only those that need to change while keeping the other parts as in their original conformation (base + backbone). This would require some manual work, but is doable with the various components in 3DNA, at least in principle. Of course, this approach is purely geometric based, thus the mutated DNA structure could be distorted or has steric-clash with protein.  You need to use molecular graphics based editing tools to fine tune the structure, and/or minimize it using energy calculations.

HTH,

Xiang-Jun

1146

General discussions (Q&As) / Re: Dealing with DNA-Protein complexes

« on: May 03, 2008, 06:46:38 pm »

Is there any way to change that ? For example, I would like to use the middle pair reference frame.

So, what's your "middle pair reference frame"? How can 3DNA know it in advance?

The 1st reference frame convention of rebuild structure should not be a problem in practice. Just as you can use frame_mol to re-orient your original PDB structure, you can do the same with structures from rebuild. As long as the two structures are in a common frame, they are comparable. And that's point.

For your own exercise and to the benefit of other forum users, I hope you could go through a simple test case, and would be willing to post back the step-by-step procedures you follow. Up to this point, only a few of 3DNA users sum up and post back. Ideally, more 3DNA users would share their experiences.

HTH,

Xiang-Jun

1147

General discussions (Q&As) / Re: Dealing with DNA-Protein complexes

« on: April 30, 2008, 10:34:46 pm »

First I'd like to thank the author and maintainer of this very useful and powerful tool, it is one thing to create such a tool but it is way harder to add some real support to it.

Thanks for your kind words about our efforts on 3DNA -- it is indeed to my great gratification to see 3DNA turned into a useful tool in the field of nucleic acid structures . Over the years, it is largely to the credit of the world-wide 3DNA user community that is driving its further refinements.

[hr:1kbblvhn][/hr:1kbblvhn]
Modeling DNA structure in a DNA-protein complex (while keeping protein structure unchanged, or RNA tertiary structures model building more generally) is an area where 3DNA can play a more active role. In principle, one can/should keep the DNA backbone conformation as they are except for the part where the base-pair parameters are varied. In this regard, it is essential to set a common reference frame so that the fragments can be properly connected. This process can't be automated in a general sense, so some purpose-specific script would be necessary.

I understand your problem in a general sense. Without seeing a specific example, this is what I would suggest you try:

• Since a structure from rebuild is always set w.r.t. the 1st base-pair reference frame, you need to firstly set your original DNA-protein complex w.r.t. its first bp frame (using find_pair/frame_mol)
• Since structures with rebuild use fixed standard backbone conformation, it is not a surprise that backbone connection would be out of normal distance, and thus not connected. By default, a cut-off distance of 4.5 A between O3'(i)--P(i+1) is used (check misc_3dna.par).

HTH,

Xiang-Jun

1148

General discussions (Q&As) / Re: Small bug in find_pair

« on: April 14, 2008, 10:31:50 pm »

As always, I welcome bug reports related to 3DNA: the more, the merrier.

The "bug" in find_pair regarding 'w' vs 'W' chain ID issue in 1VSP is well expected, though this is the first case reported. In 3DNA, all the atom names, residue names, and chain ID characters are converted to upper case, so 'w' and 'W' is treated as the same. Thus, running find_pair against this entry gives expected result.

Making 3DNA case-sensitive with regard to chain ID is not a big deal. However, do you know of any PDB documentation showing that upper/lower case makes a difference for chain ID? How about residue name, or even the 4-letter PDB id? Did you also analyze this entry with other programs, e.g., Curves, FreeHelix? How do they deal with the chain ID issue? More generally, in all the PDB/NDB entries, how many of them have chain IDs that differ only in upper/lower cases as 'w' vs 'W' for 1VSP? In my understanding, this issue may well be due to the one letter chain ID limit in PDB format itself.

HTH,

Xiang-Jun

1149

General discussions (Q&As) / Re: Baselist.dat

« on: April 09, 2008, 10:01:47 pm »

Hi Pascal,

Glad you noticed the size limitation of base list. In v1.5, which is the one currently being used, the upper limit was set to 512, and that explains the differences with the two baselist.dat files your attached. Back in around year 2000, I thought 512 would be large enough when I processed all the NDB entries. Indeed you are the first user to uncover this limit!

As far as so many unrecognized base residues as in your case, it is normal and intended. In principle, one could auto-detect the uncommon residues to keep 3DNA running without bothering with the baselist.dat file. However, as a design guideline, I have put several "check-points" in the 3DNA pipeline so users have more control, and can know what's going on. You could write a utility program to facilitate your job. If you do go that way, you might want to contribute back your work so others can benefit from your effort.

In the coming release of 3DNA v2.0, I have an up to date baselist.dat file for all the NDB entries up to March 2008, and of course, the 512 upper limit is gone. Sorry, No specified release date yet!

HTH,

Xiang-Jun

1150

Related topics / What users (objectively) have to say about 3DNA

« on: March 24, 2008, 10:23:21 pm »

Occasionally, just out of curiosity, I check the log of visitors to the 3DNA website. By following the links, I found some nice comments on 3DNA. As a humble person, I feel gratified to read them. I believe these comments reflect more objectively users' real experience and feelings about 3DNA.

Additionally,  over the years, I have received many compliments regarding 3DNA through e-mails.  I understand from experience, however, that people are more generous when they say kind words privately,  especially when asking for help  , than in public.

On the other hand, if you find any negative comments/notes on 3DNA on the internet, please add them here as well: I am always interested in improving 3DNA in ways that make sense to me.

Listed below is a sample of the nice comments about 3DNA that I happened to find on the internet (follow the link at the top of each item to see its original source).

[added: October 1, 2009] Re: [ccp4bb]: protein topology diagram, references for DNA and sugar conformation (Michael Sierk http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html)

[added: April 8, 2008] Re: [ccp4bb] DNA building program (Mensur Dlakic; Tue, 12 Aug 2008 15:50:41 -0700)

Depends for what you need the program. If you want rigorously built DNA molecule, I suggest 3DNA:

http://rutchem.rutgers.edu/~xiangjun/3DNA/

I have a program that may be better for visualizing built DNA molecules, but is not as rigorous when it comes to reconstructing DNA bases from parameters. Here are few screenshots:

http://www.homepage.montana.edu/~mdlakic/software.html

Excerpt from [ccp4bb]: Stretching Modelled B-DNA - Programs (Balvinder Dhaliwal; Tue, 10 Apr 2007 20:14:50 -0700)

Thank you for the prompt replies. I was able to generate B-DNA models of
varying pitch.
Two of the more versatile tools for manipulating nucleic acid structures
are:-

i)      NAMOT (suggested by William Scott, UCSC); download at
http://namot.lanl.gov/<https://exchweb.bcm.tmc.edu/exchweb/bin/redir.asp?URL=http://namot.lanl.gov/>

ii)     3DNA (suggested by Nicola Abrescia, Strubi, Oxford); download at
http://rutchem.rutgers.edu/~xiangjun/3DNA/<https://exchweb.bcm.tmc.edu/exchweb/bin/redir.asp?URL=http://rutchem.rutgers.edu/%7Exiangjun/3DNA/>

                                                     Balvinder Dhaliwal.
(Baylor College of Medicine, Houston, Tx.)

From Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, University of Utah: "Re: AMBER: internal coordinates "

my recommendation is to use another program
to build the helices.

3DNA - http://rutchem.rutgers.edu/~xiangjun/3DNA/

  A nice program by Xiang-Jun Lu that not only can analyze
  nucleic acid structure well, but generate models with
  fiber or user supplied parameters for arbitrary twist or
  alteration of helicoidals...

NAB - nucleic acid builder "language" by Dave Case's group, ...

Learning either one (or both) of these will be significantly more general and
useful than trying to reverse engineer nucgen...

From John E. Kerrigan, Ph.D. (Robert Wood Johnson Medical School, UMDNJ): " [gmx-users] pdb files of DNA"

Hmmm...

Try using 3DNA, a program developed by Wilma Olson's group at Rutgers for
analyzing and cleaning up PDB files of DNA/RNA structures.  See
http://rutchem.rutgers.edu/~xiangjun/3DNA/ for more info and download.

3DNA is to nucleic acids what procheck is to proteins for analysis.  Very
handy.

Enjoy 3DNA!

John

-----------------------------------------
John E. Kerrigan, Ph.D.
Robert Wood Johnson Medical School, UMDNJ
675 Hoes Lane
Piscataway, NJ 08854  USA
-----------------------------------------

From Ho-Leung Ng (UC Berkeley)  "[ccp4bb]: programs for DNA conformation analysis"

Curves: http://www.ibpc.fr/UPR9080/Curindex.html

Freehelix: http://ndbserver.rutgers.edu/NDB/ftp/ND ... eehelix98/

3DNA:http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html


   I recommend 3DNA. Cheers!


Ho-Leung Ng
UC Berkeley

3DNA has been selected as an "Essential and helpful software" by [url=http://www.biomedscience.co.uk/]http://www.biomedscience.co.uk/[/url].

Recommended by Michael Banck for DNA molecular building at CCL mailing list

Re: CCL:dna molecular building

    * From: Michael Banck <banck \at// donjuan.stud.chemie.tu-muenchen.de>
    * Subject: Re: CCL:dna molecular building
    * Date: Mon, 7 Oct 2002 13:23:18 +0200

Hi,
 > I would like to know if there is any dna molecular building free
 > program that, providing the nucleotide sequence, it outputs
 > a first approximation to dna molecular moldel, in PDB format,
 > if possible.
 have a look at
 http://rutchem.rutgers.edu/~xiangjun/software.html
 or
 http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html
 hope that helps,
 Michael
 

Recommended by Jeffrey Nauss (Ph.D., Lead Training Scientist,  Accelrys) for DNA structural analysis at CCL mailing list

CCL: Windows-based software for the analysis of the DNA structure

    * From: Jeff Nauss <jnauss*|*accelrys.com>
    * Subject: CCL: Windows-based software for the analysis of the DNA structure
    * Date: Fri, 26 Jan 2007 05:18:54 -0800

 Sent to CCL by: Jeff Nauss [jnauss__accelrys.com]
 owner-chemistry]~[ccl.net wrote on 01/26/2007 12:42:24 AM:
 > Sent to CCL by: "Patrick  Pang" [skpang::ctimail.com]
 > Dear all,
 >
 > Would you suggest software for the analysis of the DNA structure (e.
 > g. major groove, minor groove, bent angle (like cisplatin binding to
 > DNA), twist angle ...) under Windows?
 You may want to check out 3DNA at URL
 http://rutchem.rutgers.edu/~xiangjun/3DNA/download.html.
 Jeff
 --
 Jeffrey L. Nauss, Ph.D.
 Lead Training Scientist
 Accelrys
 10188 Telesis Court, Suite 100
 San Diego, CA 92121-4779
 Phone: +1-858-799-5555
 Fax: +1-858-799-5100
 http://www.accelrys.com/services/training/
 

Xiang-Jun

1151

General discussions (Q&As) / Re: 3DNA on Red Hat Linux WS v5

« on: March 24, 2008, 10:06:45 pm »

Hi,

Since I do not have direct access to Red Hat Enterprise Linux WS v5 (EM64T), which appears to be 64 bit, I can't give you a definite answer as to if the current distributed 3DNA Red Hat Linux 7.3 version (32 bit) works. I'd assume that as long as you hardware is Intel-based, it might work. Please have a try and let us know how it goes.

HTH,

Xiang-Jun

PS. I have moved your post from "Related topics" section to this section

1152

General discussions (Q&As) / Re: SwS : Solvation web Service for nucleic acids

« on: March 17, 2008, 11:04:17 pm »

Hi Pascal,

Thanks for your nice words about the 3DNA v2.0 website: it is actually not ready for public release yet ...

As you know, I have been continuously improving 3DNA both on its internal algorithm and on the website, based mostly on users' feedback. I have been working/talking about 3DNA v2.0 for quite a while, and hopefully it could be released around the summer.

As regard to the possible impact of v2.0 on your SwS server (or other related tools making use of 3DNA), I am confident to say life can only be better. Of course, some minor changes would be necessary. In due course, I might ask for some pre-release testers from the community. Overall, the design principles still hold solid: the improvements are mostly internal, or with added functionality.

I have created a new section titled "Links to other related resource". You may want to add a post with link to your SwS server. I am hoping other users can help add more links.

Best regards,

Xiang-Jun

1153

General discussions (Q&As) / Re: Global linear helical axis calculation in 3DNA

« on: March 13, 2008, 08:02:55 pm »

Hi Kateryna,

Thanks for your feedback and for summarizing the issue so clearly: Other users will certainly benefit from your experience.

In the spirit of community, everyone should try to contribute as much as possible. You have set up a good example and hopefully more 3DNA users would follow your lead.

Xiang-Jun

PS. I have sent you an email with PDF attachments of my SCHNAaP/SCHNArP papers.

1154

General discussions (Q&As) / Re: Global linear helical axis calculation in 3DNA

« on: March 12, 2008, 10:12:29 pm »

Hi Kateryna,

You can verify the output from 3DNA by adding the two lines into the PDB structure file, and visualize it using e.g., RasMol.

Code: [Select]

HETATM 9998  XS    X X 999      -0.000  -0.000   0.000
HETATM 9999  XE    X X 999      -0.000  -0.000 -30.375The "equivalent C1' and RN9/YN1 atom pairs" are defined with reference to the SAME strand. Thus the algorithm applies to single stranded DNA/RNA as well. You can find further details in my SCHNAaP paper: 3DNA uses exactly the same procedures.

If you are really interested in an implementation, please have a look at the well-known FreeHelix/NewHelix program from Dr. Dickerson, downloadable from the NDB website.

HTH,

Xiang-Jun

1155

General discussions (Q&As) / Re: problems with stacking parameters of a MD-history

« on: March 07, 2008, 07:26:15 pm »

Hi Miguel,

Now I understand the problem you face. If you search the forum, you will find a similar thread on this issue.

Basically, since all the MD trajectories correspond to the same base-pairing patterns (just as the different NMR models in an ensemble), you do not need to run "find_pair" for each structure. In fact, you could simply use the same paring information for each structure by just changing the first two lines in what would be the "find_pair" output. In other words, prepare an input file to "analyze" directly -- as if you do not have access to "find_pair".

HTH,

Xiang-Jun