Messages

1551

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

1552

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

1553

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

1554

General discussions (Q&As) / 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.

1555

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

1556

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

1557

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

1558

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

1559

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

1560

General discussions (Q&As) / 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

1561

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

1562

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

1563

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.

1564

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

1565

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

1566

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

« on: March 06, 2008, 07:38:44 pm »

Hi Miguel,

As suggested in the forum welcome message, please provide a (minimum) reproducible example so others can understand exactly what you mean in order to help you out.

Xiang-Jun

1567

General discussions (Q&As) / Re: 3DNA ppc64 GNU/linux architecture

« on: March 04, 2008, 10:04:41 pm »

Dear Alberto,

Thanks for using 3DNA and your kind words about it!

Sorry for not being able to get back to you sooner. Since I do not have direct access to such an OS/Architecture, I have tried to contact some of my friends, hoping to get a positive answer for you. However, I could not get it.

Over the past few years, I have received many requests for a compiled version of 3DNA on an OS (e.g., Intel-based Mac OS X) which I do not have a hand on. Since 3DNA is distributed only in binary form, to really solve this problem,  I would propose here that some of you offered me access to your system by setting me an account. Of course, this account would be used exclusively for compiling 3DNA so that you can benefit, and possibly others as well. Hopefully this would be a long term collaboration since I will mostly likely need to fix bugs and add more functionality for future release of 3DNA.

3DNA is widely used by the community, as evidenced by the citations it receives. Yet many of its applications, especially those for RNA structures, are still heavily underused. As much as I would like to maintain and develop it further, however, I can only work on it strictly in my spare time. Unfortunately, without additional support I will have only limited resources!

Xiang-Jun

1568

General discussions (Q&As) / Re: helical Parameters of a Modified nucleic acids

« on: February 15, 2008, 11:53:00 pm »

Hi Mathew,

I have checked the files you uploaded. There are a few issues that are needed to be clarified to run 3DNA against your XDNA structure:

• Each Atomic_?.pdb file must be set with regard to the standard base reference frame, not just taken directly from a PDB file, as in your four attachments. Have a look (e.g., using RasMol of Atomic_A.pdb with the 3DNA distribution to see an example).
  
• For 3DNA to take a residue as a nucleotide, it must contain at least a six-membered ring with standard atom names common to A/C/G/T/U etc, including the " N1 " atom. In you modified Y bases (Atomic_Y-xty.pdb, Atomic_Z-xcs.pdb and Atomic_W-xae.pdb), you have atom " N  " in place of " N1 ". In your cent02.pdb file, you also have atom " ND " in stead of " N1 " in residue XCS. That's why thay are not recognized by 3DNA. The modified R base, Atomic_X-xga.pdb, is fine.
  
• So to get to the bottom of it, you need to manually edit your cent02.pdb file to change " N  " and "  ND " to " N1 ", which I have done and attached as cent02_N1.pdb. Your Atomic_X-xga.pdb does not conform to PDB format (check Chain ID column), and you need to manually change atom name " N  " to " N1 " in the other 3 Atomic_?-???.pdb files. I have modified "std_base" with option "-fit" to set a nucleotide with regard to the standard base reference frame to be used with 3DNA, and I have attached the re-oriented bases as Atomic_r.pdb and Atomic_y.pdb. You could also use Atomic_R.pdb and Atomi_Y.pdb, but the small case letter would lead 3DNA print out diagnostic message.
  
• You do not need to have a separate Atomic_?.pdb file for each modified base. In your case, two should be enough, and the updated baselist.dat is as follows:
  
  Code: [Select]
  # for XDNA residues from Mathew
XTY     y
XCS     y
XT5     y
XAE     r
XGA     r
XA5     r
DT3     t
DA3     a
• I have also attached the 3DNA 'analyze' output file cent02_N1.out (renamed cent02_N1.txt so it can be attached) for your reference.
  
• As I said in my previous email, I helped another 3DNA user on XDNA a while ago, and here is the URL for some of the info I provided: http://rutchem.rutgers.edu/~xiangjun/3D ... /xdna.html. Please download the updated 'std_base' program (Linux version) there. In the coming new release of 3DNA v2.0 (no specific date yet!), the "-fit" option comes as built in.

HTH,

Xiang-Jun

1569

General discussions (Q&As) / Re: helical Parameters of a Modified nucleic acids

« on: February 04, 2008, 11:04:42 pm »

Hi Mathew,

Thanks for your cooperation. I am aware of the xDNA story, and actually helped a 3DNA user on a modified purine a while ago. I need to dig it out -- it is buried in somewhere... Now you see the importance of this forum!

I am pretty occupied right now, but I will get back to you about your modified bases when I get time. Please check back in a week or so.

Xiang-Jun

1570

General discussions (Q&As) / Re: helical Parameters of a Modified nucleic acids

« on: February 03, 2008, 09:05:22 pm »

Thanks for adding the attachments -- now the problem becomes quite clear.

Your modified bases, with an additional benzene ring, are so different from the normal cases where the modifications are on the exocyclic atoms, or some of the base ring atoms,  that the mechanism provided with 3DNA (baselist.dat") is no longer applicable.

For example, for residue #3 (XTY, a modified pyrimidine) there is no "N1" atom but a "N" atom. Moreover, it is the C8 atom on the benzene ring that connects to the sugar, not the normal "N1" atom.

If you attach all of the modified Atomic_?.pdb files, I would like to look further: maybe I could make some modifications to the code to incorporate these dramatic changes.

Hope this clarifies the issue.

Xiang-Jun

1571

General discussions (Q&As) / Re: helical Parameters of a Modified nucleic acids

« on: February 02, 2008, 12:58:17 pm »

Hi Mathew,

Thanks for using 3DNA. As suggested, could you provide us a minimal reproducible example (using attachment) so others see clearly what's going wrong? I understand your description of the problem, but need more details to provide you a solution.

Xiang-Jun

1572

General discussions (Q&As) /

« on: November 17, 2007, 07:53:21 pm »

Hi Yurong,

3DNA uses a set of simple, pure geometric criteria, for locating all possible base-pairs and double helical regions. The helical regions are defined from a base-stacking prospective, thus continuous and quasi-continuous (or no backbone at all) helices are handled in exactly the same way. The detailed underlying algorithm will become clear when I find time to write a paper on it and get the work published. Before that happens, you can simply acknowledge 3DNA for your helical region findings.

Among the two parameters you listed (which are made explicit in 3DNA v2.0 to be released soon -- following a new publication on 3DNA), only "helix_break" is relevant here. The other one is a criterion to decide if the analyzed structure is strongly curved. It is used to decide if to ls-fit a helical axis, as shown in section "Global linear helical axis defined ...", and to calculate a set of global parameters.

HTH,

Xiang-Jun

1573

General discussions (Q&As) /

« on: November 02, 2007, 01:10:21 am »

The two files you uploaded to the 3DNA server did help clarify the issue.

The negative Rise and strange tilt etc parameters are all related to the 6th G+G pair: the syn-G on strand I (X:...8_:[..G]G) has reversed "face" (base orientation) relative to others. The bp frame z-axis direction follows that of strand I base (the leading strand). Have a look at file "ref_frames.dat" following running the command (I am using "Ganti_Gsyn.pdb" as the PDB file name):

Code: [Select]

find_pair Ganti_Gsyn.pdb stdout | analyzeYou will see:

Code: [Select]

...     5 U-A ...
   27.5971    26.4873    48.4652  # origin
    0.7980    -0.6022     0.0226  # x-axis
   -0.5501    -0.7432    -0.3809  # y-axis
    0.2462     0.2915    -0.9243  # z-axis
...     6 G+G ...
   28.7994    26.9129    45.4857  # origin
    0.9194    -0.3494     0.1807  # x-axis
    0.2865     0.9096     0.3009  # y-axis
   -0.2695    -0.2249     0.9364  # z-axis
...     7 A-U ...
   31.2226    28.5432    44.1020  # origin
    0.0211    -0.9974     0.0687  # x-axis
   -0.9847    -0.0326    -0.1714  # y-axis
    0.1732    -0.0641    -0.9828  # z-axis
When two z-axes have opposite directions as in the cases here for the 5th UG/GA (a "blocview" generated structure is attached) and 6th GA/UG steps, the mean z-axis of the middle-frame is not well-defined, leading to the "strange" step parameters you noticed. Nevertheless, this set of parameters can still be used to rigorously rebuild the structure.

In such case, we could reverse the z-axis of the 6th G+G pair, making it pointing in the same direction as other bases along the strand. This will ensure that rise will be positive. However, there are some side-effects with this approach: for one thing, structure "rebuilding" won't work as before; secondly, when taking the 5th and 6th steps separately, there is an ambiguity as to which z-axis should be reversed. For these reasons, I prefer to keep the program as is.

Now if you think about it, the "strange" numbers are actually a good thing: it pinpoints the special structural features in this region, which is not directly comparable to other steps. As with any software tools, it is not just about getting the numbers, but most importantly understanding what the numbers really mean.

The "strange" numbers are directly tied to the choice of base-centered reference frame. The base-pair normal and RC8-YC6 based reference frame as used in SCHNAaP/CEHS (which follows NewHelix) is more intuitive. As a matter of fact, 3DNA also include a utility program "cehs" which calculates authentic SCHNAaP/CEHS parameters. Run it as follows:

Code: [Select]

find_pair Ganti_Gsyn.pdb stdout | cehsand check file "Ganti_Gsyn.outc".

For your structure, please also check the section titled "Global linear helical axis defined ..." from 3DNA "analyze" output. The global parameters based on C1'-C1' vectors make sense to me: it is these C1'-C1' vectors that show the periodicity, not being disturbed by the G+G pairs.

HTH,

Xiang-Jun

PS. The attached image was generated as follows:

Code: [Select]

find_pair Ganti_Gsyn.pdb stdout | analyze
ex_str -5 stacking.pdb s5.pdb
blocview -o -i=s5.png s5.pdb

1574

General discussions (Q&As) /

« on: October 30, 2007, 08:37:53 pm »

Thanks for using 3DNA and posting your question at the forum.

Which version & commands are you using? Could you provide me a working example so I can reproduce your problem? As always, a minimal reproducible example is far more effective than general remarks.

At the base-pair level, 3DNA differentiates M-N vs M+N type pairs:

More generally, when the two bases (M and N) forming a pair have opposing faces, the scalar product of their z-axes is negative. 3DNA designates such pairs, e.g. Watson–Crick A–U, A–T and G–C pairs, as M–N with the ‘–’ symbol used to emphasize the opposing directions. If the M and N bases in a pair share the same face, such as in the Hoogsteen base pair in Figure 2b, the pair is recorded as M+N, with the ‘+’ symbol used to emphasize the similar directions of the bases.

At the dinucleotide step level, it also checks the z-axis directions to calculate reasonable parameters (as in a structure with B-Z junction, implemented in v2.0).

A negative rise is not expected for a reasonable helical structure. Before seeing your structure, however, I don't think I could provide you with a concrete explanation.

Xiang-Jun

1575

General discussions (Q&As) /

« on: October 28, 2007, 11:50:43 pm »

As Yurong pointed out, the "poc_haxis.r3d" file is produced when "analyze" finds the structure being analyzed is not "too curved" (check "misc_3dna.par" for default setting of the parameter). It corresponds directly to the "Global linear helical axis defined ..." section from the "analyze" main output file. It does not matter if the helical region is "quasi-continuous" or not.

To make it more concrete, here is an example:

Code: [Select]

find_pair bdl084.pdb stdout | analyzeYou will get file "poc_haxis.r3d" with contents as follows:

Code: [Select]

###
### Linear global helical axis if not strongly curved
#5
#   17.536   25.713   25.665    9.424   12.911   15.677   -9.080    9.424    1.000    0.000    1.000
#5
#   17.536   25.713   25.665    6.368   12.911   15.677   -9.080    6.368    1.000    0.000    1.000
#5
#   17.536   25.713   25.665    5.849   12.911   15.677   -9.080    5.849    1.000    0.000    1.000
5
   17.536   25.713   25.665    0.060   12.911   15.677   -9.080    0.060    1.000    0.000    1.000Check also the following section from "bdl084.out":

Code: [Select]

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.30(0.52)
Helix:    -0.127  -0.275  -0.953
HETATM 9998  XS    X X 999      17.536  25.713  25.665
HETATM 9999  XE    X X 999      12.911  15.677  -9.080
Average and standard deviation of helix radius:
      P: 9.42(0.82), O4': 6.37(0.85),  C1': 5.85(0.86)
BTW, the poc in file "poc_haxis.r3d" stands for P (phosphorus), O4', and C1' atoms.

HTH,

Xiang-Jun