Messages

1451

General discussions (Q&As) / Re: 3DNA version 2.0

« on: April 28, 2010, 06:54:57 pm »

Welcome to join the forum! You (and every subscriber) are welcome to post any question that is related to the 3DNA software package, just remember to follow common-sense rules.

Xiang-Jun

1452

General discussions (Q&As) / Re: non planar base pairs

« on: April 17, 2010, 09:44:02 pm »

Hi Pascal,

This is clearly posed question.

In file "misc_3dna.par", there is the following section:

Code: [Select]

#   maximum angle between base normals (in range 0..90)
<max_plane_angle>65.0</max_plane_angle>In your specific case, setting the number from the default 65.0 degrees to 60.0 will solve your problem.

For more details, please see FAQ "How to fix missing (superfluous) base pairs identified by find_pair?"

[hr:2mhasqib][/hr:2mhasqib]
Furthermore, in our recent GpU paper (see also my blog post: "What's special about the GpU dinucleotide platform?"):

We chose the following set of stringent parameters to ensure that the geometry of each identified base pair is nearly planar and supports at least one inter-base H-bond: (i) a vertical distance (stagger) between base planes ≤1.5 Å; (ii) an angle between base normal vectors ≤30°; and (iii) a pair of nitrogen and/or oxygen base atoms at a distance ≤3.3 Å.

HTH,

Xiang-Jun

1453

General discussions (Q&As) / Re: find_pair and HETATM

« on: April 16, 2010, 09:11:51 pm »

Hi Pascal,

Thanks for your verification. We all learn from mistakes, and our change of views serves as another example of the ever-refining process (kaizen; improve; 改善) that is required to keep a (software) product alive. As a general rule, I have never deleted or changed posts from users. I lock a thread when I believe the topic is finished.

3DNA does not read CONECT records from PDB, which is incomplete (by design), inconsistent, and unreliable. Instead, 3DNA implements an algorithm to decide if two atoms are covalently connected based on pure geometrical criteria. If you want to discuss this topic further, please start a new thread.

Best regards,

Xiang-Jun

1454

General discussions (Q&As) / Re: find_pair and HETATM

« on: April 15, 2010, 11:12:25 pm »

Hi Pascal,

Could you provide a step-by-step reproducible example? At the bare minimum, please attach the PDB file you used to generate the image. I checked 1VBZ, but failed to repeat the problem you reported  -- I could not find any BA atom in file "allpairs.pdb".

If verified, it is certainly a bug and I won't hesitate to fix it.

Best regards,

Xiang-Jun

1455

General discussions (Q&As) / Re: A little background on the -negx option and rebuild of s

« on: April 13, 2010, 09:02:38 pm »

Hi Mauricio,

You have touched a subtle point, indeed you are the first to post a question on the -negx option of "rebuild". I do not have time to go into details (due to a couple of deadlines), but here are my quick answers to your questions.

When 3DNA finds a negative twist it reverses the direction of the x- and z-axes.
I would like to ignore this for all cases since I don't have Z-RNA conformations.
Is there another way besides using the -negx command?

The -negx is designed for that specific purpose.

Also, I might be missing out the deeper reason for the default behaviour of reversing the axes directions, I understand the reasons for base-pairs as you explain in your NAR paper of 2003 (page 5109), but I don't understand fully the reasons for the step case. Could you please expand a little bit more on this explanation, or point me to some of your papers which I might have overlooked?

Have a look of my SCHNAaP/SCHNArP papers (J Mol Biol. 1997 Oct 31;273(3):668-80; J Mol Biol. 1997 Oct 31;273(3):681-91), where the "a" and "r" are the origins of the "analyze" and "rebuild" programs in 3DNA (both algorithm-wise and in code base).

HTH,

Xiang-Jun

1456

General discussions (Q&As) / Re: find_pair and HETATM

« on: April 09, 2010, 11:45:18 pm »

Hi Pascal,

Finally we tested your option -attach that works really fine. A lot easier for us. now!

Glad to hear.

The .ana output looks less interesting to us than our workaround since it s lacking some info that we get by rewriting the find_pair output with -pz to a new output readable by analyze. At a later stage, it would be nice to have a complete output for analyze comming out from "find_pair -pz".

Could you be more specific so I (or others who are interested in) can see what exactly you want to achieve? As mentioned before, the "-p" option of "find_pair" was incompatible with "analyze" by design for a valid reason. I understand that 3DNA serves also as a tool kit, being used in "unexpected" ways. I am open and I'd be more than willing to be convinced to new ideas. As a design principle, though, I change 3DNA only in ways that make sense to me. When adding a new feature (excluding experimental and undocumented one, of course), I have always asked myself this question: will I be able to give user a concrete explanation or quickly acknowledge (and possibly fix) a bug? As a supplement and complement, users are always welcome to share their tricks and scripts with the community in the Users' contributions section.

Was just also looking at the RN9-YN1 and RC8-YC6 info you provide in the analyze output. The labeling of this columns seems not appropriate since you do not consider the YY and RR base pairs occurrences, do you ?. The YN1-YN1 and RN9-RN9 columns are missing apparently. From my point of view, the C1'-C1' and the two lambdas provide all the needed info.

Again, be specific (using a concrete example) to show where (you think) is wrong. As fas as I could tell, even though the column headers are always labeled RN9-YN1 and RC8-YC6 (intentionally), 3DNA should handle YY and RR pairs properly. Please verify.

Xiang-Jun

1457

General discussions (Q&As) / Re: find_pair and HETATM

« on: March 29, 2010, 08:13:54 pm »

Hi Pascal,

I have finally found time to update "find_pair" to fulfill your requests:

• I have added an option "-attach=STRING": where STRING is case-insensitive, and if it is "off", "no" or "0", then the attached HETATM groups will not be added to the output coordinate file.
• With the "-p" option, I have added an output file named "allpairs.ana" that can be fed into "analyze".

See my email for detailed instructions to update. Please post back here to confirm that my modifications work as advertised, or if you have further questions.

Xiang-Jun

1458

General discussions (Q&As) / Re: find_pair and HETATM

« on: March 27, 2010, 04:42:22 pm »

Hi Pascal,

What OS do you use? I will compile a version of 'find_pair' that works for you. As with v1.5, I will keep the currently distributed v2.0 as is, unless I notice some significant issues.

Xiang-Jun

1459

General discussions (Q&As) / Re: find_pair and HETATM

« on: March 24, 2010, 10:01:23 pm »

Dear Pascal,

Regarding our last post, we would also really appreciate if you could at one point consider providing an output for "find_pair -p" (using the -p option) that could be run through analyze (its not the case right now). This would be also more than helpful for us.

I may consider adding a new output file from "find_pair -p" that can be fed directly into "analyze" when I turn into "programming mode" to address your HETATM request. In the meantime, it should be straightforward to write a script that parses the output file from "find_pair -p" to feed into "analyze". More generally, as demonstrated in the 2008 Nature Protocols paper, 3DNA should be taken as a toolset that, when combined with other programs, can be explored with command line scripts to fulfill specific needs.

Yet, I understand that you are really busy combining several jobs.

As mentioned several times in the forum and on the 3DNA websites, and made clear in my blog post titled "On maintaining the 3DNA forum", my supporting of 3DNA and the forum is purely on a voluntary basis, not a "job" duty at all:

Over the past few years, maintaining the 3DNA forum (i.e., answering questions, performing administrative tasks) has taken up a significant amount of my spare time. Sometimes it could be quite demanding, especially because I need to pay great attention to details. Overall, though, it is a valuable experience, and I feel that the time is well-spent: 3DNA has been continuously refined and more widely used; my knowledge of nucleic acid structures (especially RNA) has been significantly sharpened; I have stayed aware of progress in related research fields and see more of the world; and I feel great pleasure in being of help to the community.

I do enjoy what I am doing with 3DNA and I have learned a lot, even from a negative comment on my effort (BTW, the thread is well worth reading):
[hr:1txo5elk][/hr:1txo5elk]

You [Xiang-Jun] clearly have the ability to avoid answers to the questions. You lecture me how to pose a question, I recommend you learn how to answer a question. I read your answers to other questions and the pattern is the same: to give as little help as possible. Still I like your program better than the other programs, so please, try to be more helpful. Do you think Wilma knows how to use this program? Maybe I should write to her?

[hr:1txo5elk][/hr:1txo5elk]

Best regards,

Xiang-Jun

1460

General discussions (Q&As) / Re: find_pair and HETATM

« on: March 23, 2010, 11:42:15 pm »

Dear Pascal,

Over the years, I have always been surprised by your sharp observations of some fine details of undocumented 3DNA features, through our extensive email communications (mostly before the 3DNA forum was set up) and your posts in the forum.

Just found out that for some base pairs, find_pair extracts some additional atoms (CA, K, TL, MG among others) and also complete modified residues like in 1MO5 (bp 12) and 2PIS (bp 9) (see attached files). Is that how it should be. Did we miss an option or misunderstand something ? This does not occur with the -a option, yet info related to modified residues are then lost.

Yes, the attached HETATM moieties (including metals, and modified nucleotides) you observed are expected, thus you did not miss any option or misunderstand something. Based on my experience with PDB format 2.x, I checked for possible linkage between a hetero group (e.g., a drug molecule) and the base residue, and added the HETATM group to the output coordinates file if it is connected to the nucleotide.

Obviously, the extra-mileage I took seems too far for your purpose. So I am considering to add a new command line option to “find_pair” that, if specified explicitly, would exclude such HETATM groups (metals, or modified residues). I am pretty busy for my job right now, but I would keep your request in mind. Hopefully, I would be able to get a working solution for you in a week (by the end of this month).

Xiang-Jun

1461

General discussions (Q&As) / Re: findpair -p and -z options

« on: March 12, 2010, 08:53:09 pm »

Hi Pascal,

The "-p" option of find_pair is for pairwise checking of all possible base-pairs, and for identifying higher-order base associations as demonstrated in the 2008 3DNA NP paper (Recipe no. 5). It was not intended to be used with analyze, as I initially added the option there. The "-z" option, on the other hand, was mostly used to decide suitable criteria of which base-pair should be included in a helical region. Its output information is far too technical for outside users.

Regarding the output parameters from the "-p" option, the header section should be of some help:
[pre:byvny7l4]Six-line information for each base-pair as follows:
   #1: Overall serial number, local serial number, paired residue numbers,
       detailed pairing residue information.
   #2: One-letter base-pair followed by six base-pair parameters (shear,
       stretch, stagger, buckle, propeller, opening). The parameters are
       with respect to the Watson-Crick base reference frame. There are
       two types of base-pair orientation: M-N means the two bases have
       opposite orientations as in Watson-Crick base-pair; M+N means the
       two bases have the same local orientations as in Hoogsteen base-
       pair. All possible base pairing patterns can then be classified
       based on the six parameters, among which shear, stretch and opening
       are most discriminative.
   #3: H-bonding information (atom pair followed by their distance).
   #4: Overall classification of the base-pair (anti-parallel vs parallel
       based on relative z-axis of the two bases, cis vs trans based on
       x-axis and C1-RN9/YN1 directions).
   #5: Relative directions of the three axes and their numerical values.
       The last 3 numbers are the angles between the glycosidic bonds, and
       the two chi torsion angles.
   #6: The actual parameters used to locate the base-pair in question.[/pre:byvny7l4]
Some of the undocumented features of 3DNA are experimental or are related to still unpublished work. I am hoping to be able to devote more efforts to research on nucleic acid structures, but it all depends.

Xiang-Jun
[hr:byvny7l4][/hr:byvny7l4]
PS. BTW, isn't FR3D sufficient for tasks related to the identification and classification of base-pairs? The FR3D webpage contains tons of information; some of which you may find helpful.

1462

General discussions (Q&As) / Re: Finding non-sequential base step parameters

« on: March 08, 2010, 07:53:39 pm »

I am wondering if it's possible to find all base step parameters

No, it is not possible. There are simply too many possibilities, e.g., for 23S rRNA in 1jj2, and most of them make no sense at all.

I am aware that I can isolate the base_step and calculate the step parameters for them

What do you mean to "isolate the base_step"? If you separate find_pair -s from analyze, you could simply play with the output file from the former to get what you want.

HTH,

Xiang-Jun

1463

General discussions (Q&As) / Re: Error Running X3DNA_setup script

« on: February 01, 2010, 11:11:23 pm »

The Perl script x3dna_setup is a simple, straightforward utility program with source code available. Apparently, you are more a Windows users, not that familiar with Linux/Unix and Perl. So it would be most helpful if you could find a local expert to help you out.

Here are some specific suggestions:

• Is x3dna_setup executable? You may need to run "chmod u+x *" in X3DNA/bin/ directory.
• What "which perl" outputs? If not /usr/bin/perl, you will need to change the first line in the script to reflect your local setting.
• Does your Perl installation have modules "FindBin" and "File::Basename"? If not, you will need to have then installed.
• What is the output of the following:
  
  Code: [Select]
  echo $HOME
echo $SHELL
and the directory of you 3DNA installation?

Since I am basically a non-Windows person, I am hoping other 3DNA users using Cygwin and MinGW would help out with more detailed instructions.

Xiang-Jun

1464

General discussions (Q&As) / Re: RNA 2D structure

« on: January 24, 2010, 07:28:38 pm »

I would like to get the secondary structure of all these 3D structures. Is it possible with 3DNA software? If so please let me know how to use that.

From a 3D RNA structure in PDB format, find_pair in 3DNA can identify all the double helical regions. Maybe that would serve as a starting point?

You may also find my blog post titled "Does 3DNA work for RNA?" relevant.

HTH,

Xiang-Jun

1465

General discussions (Q&As) / Re: 3DNA

« on: January 23, 2010, 08:36:27 pm »

Hi I buy the software 3DNA AND I can not access the download add-on WORLD, can you help me :roll:

Where did you buy "the software 3DNA" :? ? This 3DNA forum is on "Topics Related to the 3DNA Software Package for the Analysis, Rebuilding & Visualization of Three-dimensional Nucleic Acid Structures", and it does not have "add-on WORLD" at all.

Xiang-Jun

1466

General discussions (Q&As) / Re: DNA Step Values for DNA Mismatches

« on: January 21, 2010, 10:33:57 pm »

...... reading file: baselist.dat ......
unknown residue DG 1 on chain E [#1]
Check the base and add one more item in file <baselist.dat>

Take the hint, and read FAQs on "How to fix missing (superfluous) base pairs identified by find_pair?" and "How to handle modified (uncommon) bases?" to see how to handle such cases.

Notice that it complains about the DG residue. As well, it is unable to produce the corresponding 2O8B.out file. I think that this is due to the unrecognized naming convention "DG" which should be written as "GUA" instead. This is why I had extracted the coordinates before and renamed them all to GUA, ADE, THY, and CYT.

Following the suggestion above, you do not need to manipulate PDB file at all. 3DNA v1.5 works in such situation as well, and this topic has been brought up in the forum before.

...... reading file: baselist.dat ......
uncommon residue ADP 936 on chain A [#1793] assigned to: a
uncommon residue ADP 202 on chain B [#1795] assigned to: a
................................................................
Instead of complaining about the DG (which I assume is "fixed" in v2.0), it complains about the ADP nucleotides which are present in the PDB file (of 2O8B.pdb, not the modified one).

Note that this is for information only. Again, reading and understanding the above mentioned two FAQs would help.

ii) They both still do NOT contain the first G-C base pair information (even with v2.0 using an unmodified PDB file downloF:..30_:[.DC]Caded from PDB.org).

I have just checked and reproduced your result with the distributed 3DNA v2.0. The missing first G-C base-pair is due to the distortion of C30 on chain F.

iii) The output format for v2.0 is slightly different from v1.5 (so my parsing script written in Perl will need to be modified)

iv) The final column in each row for each base step is different (-1.13 vs. 1.03). I think I read somewhere that this value is simply being calculated differently?

v) The base-pair criteria used appears slightly different.

Over the time, there are some internal changes in find_pair. Moreover, contents following "#" are for information only, undocumented, and are subjected to changes.

4) I will try modifying the helix break parameter as you had suggested (just for experience) but from what you said, it looks like I could just extract the pertinent information directly from the "bp_step.par" file without having to do that since it will always include a complete set of parameters. Is that correct?

If you are just interested in getting the numbers, yes, 'bp_step.par' contains all the base-pair and step parameters.

HTH,

Xiang-Jun

1467

General discussions (Q&As) / Re: DNA Step Values for DNA Mismatches

« on: January 17, 2010, 05:45:42 pm »

Hi Sean,

Thanks for the well-formulated question. I am impressed that you noticed the fact that a set of step parameters is omitted in 3DNA main parameters file (*.out) of 2o8b, but available in file 'bp_step.par'. In my support of 3DNA over the years, you are the first who has dug into this detail.

First, a clarification:

After extracting the DNA coordinates and analyzing it with 3dna, ...

Did you that you do not need to first perform "extracting the DNA coordinates" from the PDB file? With "find_pair", you can analyze a nucleic acid structure directly from a PDB file. See FAQ for an example.

Now to your specific questions:

Code: [Select]

5 GC/GC -0.20 0.24 3.45 2.85 -2.55 38.63
6 CG/TG ---- ---- ---- ---- ---- ----
7 GC/GT 3.87 0.83 3.32 -11.26 0.08 6.18I should point out that step 6 is where the G-T mismatch is located but I don't understand why the parameter values are missing.

If you check carefully the output file from "find_pair" (BTW, your output file apparently lacks the first G-C base-pair, why?),

Code: [Select]

2o8b.pdb
2o8b.out
    2         # duplex
   15         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   30  0 #    1 | ....>E:...1_:[.DG]G-----C[.DC]:..30_:F<....  1.14  0.36 14.09  9.30 -0.44
    2   29  0 #    2 | ....>E:...2_:[.DA]A-----T[.DT]:..29_:F<....  0.89  0.82 26.82  9.09 -1.13
    3   28  0 #    3 | ....>E:...3_:[.DA]A-----T[.DT]:..28_:F<....  0.23  0.03 18.38  9.24 -3.78
    4   27  0 #    4 | ....>E:...4_:[.DC]C-----G[.DG]:..27_:F<....  0.78  0.19  8.59  8.93 -3.40
    5   26  0 #    5 | ....>E:...5_:[.DC]C-----G[.DG]:..26_:F<....  0.56  0.29 17.33  9.24 -3.00
    6   25  0 #    6 | ....>E:...6_:[.DG]G-----C[.DC]:..25_:F<....  0.29  0.27 19.28  9.01 -3.20
    7   24  9 #    7 x ....>E:...7_:[.DC]C-----G[.DG]:..24_:F<....  0.22  0.01 24.18  9.04 -3.55
    8   23  0 #    8 | ....>E:...8_:[.DG]G-**--T[.DT]:..23_:F<....  5.22  0.31 43.28  9.87  7.00
    9   22  0 #    9 | ....>E:...9_:[.DC]C-----G[.DG]:..22_:F<....  0.44  0.33 20.98  8.84 -2.85
   10   21  0 #   10 | ....>E:..10_:[.DG]G-----C[.DC]:..21_:F<....  0.41  0.39 10.80  9.05 -3.28
   11   20  0 #   11 | ....>E:..11_:[.DC]C-----G[.DG]:..20_:F<....  0.26  0.01 12.86  9.06 -4.07
   12   19  0 #   12 | ....>E:..12_:[.DT]T-----A[.DA]:..19_:F<....  0.85  0.47 11.88  8.95 -2.62
   13   18  0 #   13 | ....>E:..13_:[.DA]A-----T[.DT]:..18_:F<....  0.53  0.18  9.30  8.85 -3.65
   14   17  0 #   14 | ....>E:..14_:[.DG]G-----C[.DC]:..17_:F<....  1.17  0.94 21.28  8.97 -0.89
   15   16  0 #   15 | ....>E:..15_:[.DG]G-----C[.DC]:..16_:F<....  1.17  0.05 37.85  8.66 -1.83
##### Base-pair criteria used:   4.00   0.00  15.00   2.50  65.00   4.50   7.50 [ O N]
##### 1 non-Watson-Crick base-pair, and 2 helices (0 isolated bps)
##### Helix #1 (7): 1 - 7
##### Helix #2 (8): 8 - 15
you will find that the structure has been broken into two helical fragments, at the middle G-T pair. If you set the helix_break parameter in file 'misc_3dna.par' (see the FAQ) from the default 7.5 Å to a larger value, e.g., 8.5 Å as below (3DNA v2.0),

Code: [Select]

#   distance criterion for helix break
<helix_break>8.5</helix_break>"find_pair" will take the whole double helix as a single unit, and the "analyze" output parameters would have included the "missing" step.

Alternatively, with default 'misc_3dna.par' parameters, you can still recover the "missing" step parameters by adding '-c' option to "analyze". Type "analyze -h" to see how it works, and yet another alternative.

In addition, I notice that another output file (bp_step.par) that contains the base-pair step parameters actually has values for the mismatch:
.............................
The (shift, slide, rise, tilt, roll) values are essentially identical in both cases with the exception of the missing values for the mismatch. What do the values in the latter case actually mean and why are they missing in the first case?

No matter how many helical regions are involved in the input file to "analyze", the fixed-named output file 'bp_step.par' always include a compete set of parameters, including the inter-helix steps. This is to ensure that "rebuild" has enough information to construct a model of the whole structure. Thus, the values in the two cases (*.out vs "bp_step.par") mean exactly the same thing; they just serve two different purposes.

HTH,

Xiang-Jun

1468

SCHNAaP/SCHNArP / Re: backbone utility program

« on: January 06, 2010, 08:49:12 pm »

I am glad that you find my SCHNArP program useful to your project.

The 1997 publication on SCHNArP mentions that there is a utility that "traces the path of the backbone by connecting the C1' or RN9/YN1 atoms in the atomic models and the sugar atoms in the schematic models." I cannot locate that utility program in the SCHNAaP/SCHNArP package.

The connection is for visualization purpose only, i.e., to help "traces the path of the backbone". As far as I can recall, the utility was initially written in Matlab, and was intended to be with used with Rasmol. The atomic models in PDB format normally do not contain explicit bond connections. So in the C version distributed, I decided to support this functionality only for the schematic models in Alchemy format; it is now integrated into SCHNArP directly.

For your verification, in the Examples/ directory, you will find several example files DNAp76[a-d].cnt which contain such "backbone" trace. I have also just run SCHNArP using DNAp76a.dat as input, and got two files: CEHS_gen.cnt and CEHS_gen.out. The attached image corresponds to CEHS_gen.cnt. It was generated with Rasmol 2.6.4. (see my blog post: http://xiang-jun.blogspot.com/2009/06/r ... sayle.html)

Note that the file DNAp76a.cnt was generated using a different base-pair BLOCK model. See README.1st and options available in BaseGeo/BLOCK*.alc files; feel free to play with it.

Also, are there source codes available that provide atomistic coordinates of the backbone sugar/phosphate atoms between 2 existing bases?

There must be such source codes available somewhere, but not in SCHNArP or 3DNA. In my understanding, given the geometry of two bases or base-pairs, there is no unique/object ways to define the backbone conformation. So in SCHNArP/3DNA, I've only provided simple rigid-body A-, or B- conformations, attached to the bases. Such approximate full atomic models with backbone could be useful as starting points for other explorations (see our 3DNA 2008 Nature Protocols paper for further explanation on this topic).

HTH,

Xiang-Jun

1469

General discussions (Q&As) / Re: Deformability of a small DNA fragment

« on: November 23, 2009, 11:38:31 pm »

3DNA does not perform energy calculations per se, but please have a look of the post "deformation energy calculation program" by Dr. Thomas Gaillard at the Users' contributions section.

If you have further technical questions, you may want to post over there: I think Dr. Gaillard would follow up.

Xiang-Jun

1470

General discussions (Q&As) / Re: From DNA sequence to DNA structure

« on: November 19, 2009, 08:23:13 pm »

The basic issue is that there is no one-to-one correspondence between DNA sequence and its 3D structure. For example, a 146-bp fragment could be in left-handed super-helical form as in nucleosomal DNA,  or other other conformations (straight or not). In the literature, there have been several bending models, each of which assigns a set of step parameters (roll, twist etc) to specific sequence (at di-, tri- or tetra-nucleotide level).

As noted in the 3DNA 2008 Nature Protcols paper (3DNA-NP):

"Thirdly, as demonstrated in SCHNArP, various DNA bending ‘rules’, with different sets of tilt/roll/twist values at the constituent dinucleotide or trinucleotide steps, can be easily incorporated within a script that transforms a sequence with an assigned ‘bending model’ into an input file that feeds into rebuild."

So overall, you are in the right direction, as far as building a DNA model is concerned. Now to your specific questions:

1. I used only dinucleotide shift, slide, rise, tilt, roll and twist parameters that download from DiProDB, but ignored Shear, Stretch, Stagger, Buckle, Prop-Tw and Opening.

The "rebuild" program in 3DNA can take two types of input, as documented in 3DNA-NP. You can ignore Shear, Stretch ... etc base-pair parameters, which will be taken as zeros.

2. I wrote a small program to generate a base step parameter file from DNA sequence just like the bp_step.par in X3DNA example.

It can be simpler, as noted above. Please see also 3DNA-NP: working through recipe #2 would clarify the issues.

3. I use rebuild program to build a 3D model by using the base step parameter file in step 2. (rebuild -atomic M1_sense.3dna M1_sense.3dna.pdb)

Yes, it is right.

Everything works fine. But when I use SPDB Viewer to visualize my model, I found some segment did not connected well (please see Picture 2.png in attached file). Is this problem can be fixed?
Or this is a viewer problem? I've tried JMol, but Jmol cannot show it properly.

That's normal. Again as noted in 3DNA-NP:

Secondly, rebuild allows for the construction of atomic-level nucleic-acid structures (‘-atomic’ option) with sugar–phosphate backbones in pre-assigned, fixed conformations (specified by standard residue files; see the FAQ section at the 3DNA website). Such models, which have precise base-pair geometry but approximate (sometimes distorted) backbone connections, provide a useful starting point and basis for analysis of all-atom simulations.

One more note, 'rebuild' generated PDB files have full CONECT records, and should display with all proper connections with RasMol. Of course, some of the O3'(i) to P(i+1) bonds would be quite long.

So, I would suggest you to download 3DNA v2.0, and play with the worked examples.

HTH,

Xiang-Jun

1471

General discussions (Q&As) / Re: NUPARM vs X3DNA twist values

« on: November 11, 2009, 08:44:18 pm »

As illustrated in Figure 3 of the standard reference frame paper [J. Mol. Biol. 313(1), 229-237, 2001], and in the section "Treatment of non-Watson±Crick base pairing motifs" of the 3DNA 2003 NAR paper (also Figure 3), the discrepancy you noticed in Twist angle between 3DNA and NUPARM is due to large Shear of the G-U Wobble pairs.

You may need to (re)read the two papers for further details. It would be helpful if you repeat your calculations with Curves+ and post back your results: I would guess that Curves+ twist angle be pretty similar to that from 3DNA.

HTH,

Xiang-Jun

PS: Please also see my blog post "How shear affects twist angle of a dinucleotide step?"

1472

General discussions (Q&As) / Re: About DNA contour length

« on: October 30, 2009, 08:57:38 pm »

I have a question when calculating the DNA contour length. Can I use the sum of Rise as the contour length and use the sum of h-Rise as the end-to-end distance? So DNA bending is measured by the ratio of the end-to-end distance and the contour length?

3DNA does not calculate DNA contour length. As far as if it is appropriate to use sum of Rise as contour length, and sum of h-rise as end-to-end distance, why not you try some examples? Using ribosomal DNA superhelix, for example, would the numbers make sense? For quantify DNA bending, there are already discussions in the 3DNA forum. You could also try Curves/Curves+ from Lavery et al.

The other question is how to analyze a pdb file that has a lot of frames in it?

I do not think I understand your point here. Could you be more specific?

Xiang-Jun

1473

General discussions (Q&As) / Re: DNA rotation cont'd

« on: October 17, 2009, 06:31:48 pm »

As I said last time on Wed Jul 08, 2009, which is quoted below:

Could you be more specific? Which command and options did you use? Preferably with a reproducible example?

Unless you provide something specific and reproducible, I honestly do not know what you are talking about. When you claim something "not work", please provide a step-by-step description what have you done (which version, program and command-line options), and what error message you received, with all necessary data files and scripts. At the concrete level, it is easy to judge something right or wrong, and I always welcome 3DNA bug reports. In my experience, failing to provide a (minimal and) producible example and not being responsive are two of the top reasons that make a online forum discussion topic difficult and unproductive.

Please read carefully README First, and the note I sent with your forum registration.

Xiang-Jun

1474

General discussions (Q&As) / Re: 3DNA calculation for Bases that have two conformers in pdb

« on: October 08, 2009, 06:58:09 pm »

This is a subtle point with regard to the ATOM or HETATM records of PDB format, and I am glad that you raised the issue. 3DNA has been designed with this in mind and works as it should.

In 3DNA v2.0, file misc_3dna.par contains the following section:

Code: PHP

1. <span class="syntaxdefault"></span><span class="syntaxcomment"># Section 2&#58; alternative location in ATOM or HETATM records
2. #   default to A or 1 (A1), and ' ' is always added
3. </span><span class="syntaxkeyword"><</span><span class="syntaxdefault">alt_list</span><span class="syntaxkeyword">></span><span class="syntaxdefault">A1</span><span class="syntaxkeyword"></</span><span class="syntaxdefault">alt_list</span><span class="syntaxkeyword">></span><span class="syntaxdefault"> </span>

Thus, by default, only ATOM or HETATM records with alternative locations (column #17) of ' ', 'A' or '1' are processed. Of course, as pointed out in 3DNA FAQ, you could modify file misc_3dna.par to use other alternative locations: 'B', for example.

HTH,

Xiang-Jun

PS:

• Every 3DNA user should upgrade to v2.0: you have nothing to lose (no backward compatibility issues) but to take advantage of a more refined piece of software.
  
• Are you sure 437D.pdb has the ATOM records you listed?
  
  Code: [Select]
  e.g from 437D.pdb
ATOM 47 O4'A G A2648 -26.371 52.168 -12.884 0.58 13.58 O
ATOM 48 O4'B G A2648 -25.879 52.221 -11.854 0.42 16.38 O
ATOM 49 C3'A G A2648 -24.982 50.605 -13.934 0.58 11.81 C
ATOM 50 C3'B G A2648 -24.120 50.873 -12.569 0.42 14.39 CI cannot find them in 437D.pdb. It is not an important point here, but it would be helpful if you can clarify the discrepancy, just for the record.

1475

General discussions (Q&As) / Re: Option not to display calculation status to screen.

« on: September 02, 2009, 11:28:37 pm »

Hi Mauricio,

Thanks for formulating your question so clearly, especially for providing an example. Browsing the forum, one would find how many times I have asked for clarifications so I can understand what a question is about, exactly.

Okay, now back to your question.

Ideally, I could have provided a -q option (for quiet, or something similar) so the output message can be suppressed. As current is with 3DNA, however, the diagnostic information is directed to stderr. This should not be a problem in real life, with the help of Unix/Linux file redirection.

Again, an example would make the point clear. So let's use 'bdl084.pdb', you need to do the following:

Code: [Select]

find_pair bdl084.pdb bp_info 2> msg1
analyze bp_info 2> msg2

# or by combining them as this
find_pair bdl084.pdb stdout 2> msg1 | analyze 2> msg2
Note I am using bash shell. For other shells, you may need to use something different. Of course, you could also play with some variants along the line.

HTH,

Xiang-Jun