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Messages - xiangjun

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1
General discussions (Q&As) / Re: buggy rebuild
« on: Today at 09:16:09 pm »
The thread has diverged from its original subject matter. To repeat my point, 3DNA 'rebuild' is working as designed, from v1.5 in 2003, upto the current v2.3. I may consider an option for PDBx/mmCIF output format, but the PDB format will stay as is.

I'm glad you've written your own code to build your DNA model. Good luck!

Xiang-Jun


2
General discussions (Q&As) / Re: buggy rebuild
« on: Today at 08:52:38 pm »
Quote
what you believe to be the only "correct" way to write a PDB file

Well, I just follow the standard PDB format, and as shown in the PDB entries from the RCSB. I have no opinon on this matter at all.

On a practical side, the source code of 3DNA is available. One can easily change f8.3 to f8.2 or f8.1, as desired. However, that will NOT solved the inherent limitation of the classic PDB format.

Xiang-Jun

3
General discussions (Q&As) / Re: buggy rebuild
« on: Today at 08:23:27 pm »
Did you notice the diagnostic message when running 'rebuild' when the structure is big? The coordinates are reset to account for f8.3 format. To verify if 'rebuild' is doing what it is supposed to do, simply 'analyze' the generated structures. It should give the parameters you start with.

So far, I am not convinced "something is really going wrong" with analyze/rebuild. What to fix? Everything is working as expected, from my perspective. It is nice to have open discussions, on the 3DNA Forum.

Xiang-Jun

4
General discussions (Q&As) / Re: buggy rebuild
« on: Today at 06:46:39 pm »
Hi Luke,

This is not a bug in rebuild but related to the limitation of the classic PDB format. You can easily verify this by checking the outputted PDB file. By reducing the number of base pairs (say to 500) in your input, you can get an expected structure in the PDB format.

Try the -xml option to output the desired structure in PDBML format, as shown below:

Code: [Select]
rebuild -atomic -xml structure-5000bp-ID0-B0-1.dat big-str.xml
HTH,

Xiang-Jun

5
It is a vague question (to me). There may be standard protocols for handing methylation or other types of DNA/RNA modifications in the MD field. I'm not a practitioner of MD simulations, and do not know "if there are force field and parameter field available for them".

As far as 3DNA is concerned, you could try "fiber" and then "mutate_bases" (plus other 3DNA utilities) to get the started. See the FAQ entry "How can I mutate cytosine to 5-methylcytosine" for the most common case.

HTH,

Xiang-Jun

6
MD simulations / Re: local helical axis vector for strongly bent DNA
« on: June 21, 2017, 09:50:24 pm »
Check the source code to get to the bottom of the technical details.

For the analysis of NMR ensembles or MD trajectories, however, manually editing 'find_pair'-generated base-pair file may be the preferred way to go, as documented for the 'x3dna_ensemble' script distributed with 3DNA.

Xiang-Jun

7
MD simulations / Re: local helical axis vector for strongly bent DNA
« on: June 21, 2017, 03:50:03 pm »
Hi Adina,

Thanks for your follow-up. Your cases occur frequently, especially in the field of MD simulations. Please have a look of the FAQ entry "How to fix missing (superfluous) base pairs identified by find_pair?".

Using your F30 as an example, the two terminal "base pairs" are too far off normal, as can be seen clearly from the attached image. Similar story happens for F29. For such cases, the 3DNA find_pair program won't detect these "presumed" base pairs. This is not a bug, but a feature by design. Users should pay close attention to these missing pairs.

You can force 3DNA to take them as pairs by manually editing the output from "find_pair" before feeding it into "analyze". The find_pair/analyze two-step procedure has been implemented in 3DNA specifically to allow for such flexibility.

HTH,

Xiang-Jun

8
MD simulations / Re: local helical axis vector for strongly bent DNA
« on: June 20, 2017, 07:54:59 pm »
Hi Adina,

Thanks for posting on the 3DNA Forum. Without seeing a concrete example, I can only guess based on experience. Let the structure (a single frame) be named sample.pdb, try the following to see if you can get what you want:

Code: [Select]
find_pair sample.pdb | analyze -c
Note the -c option which treats the detect double helix as a continous unit.

HTH,

Xiang-Jun

9
The error message shows some variables (e.g., LIBFFTW etc) are not set. Presumably you need to install additional libraries, which are nevertheless not required by 3DNA per se. You may need to contact the author(s) of do_x3dna for further details.

Xiang-Jun

10
MD simulations / Re: Analysis of Amber .mdcrd File
« on: June 15, 2017, 12:07:32 pm »
3DNA starts from the standard MODEL/ENDMDL ensemble PDB format, as for NMR structures. It does not work directly from an AMBER trajectory file, or other specialized MD formats. However, it should be feasible to convert MD-specific formats to the standard PDB ensemble format. For torsional anlge calculations, you may want to try DSSR (which has the --nmr option).

Alternatively, you may try do_x3dna, or Curves+.

Xiang-Jun

11
Quote
Have you ever seen something like that? Is it because the presence of a flipped base makes impossible to calculate the dimer step parameters? Should I omit thie data points at the central region?

Yes, such distortions are common in DNA-protein complexes (e.g. complexes of DNA methyltransferase with DNA). The flipped base does not form a base-pair anymore, as can be seen clearly using Jmol/PyMOL, and thus not reported by the 3DNA find_pair program.

You could force the 3DNA analyze program to calculate step parameters involving flipped bases. See FAQ entry How to fix missing (superfluous) base pairs identified by find_pair?, and the 3DNA 2008 Nature Protocols paper. However, such parameters do not make 'intuitive' sense, even though they can be used to rigorously rebuild the relative base geometry of the original structure.

You may simply omit the point in the central region, with some note in the text

HTH,

Xiang-Jun

12
General discussions (Q&As) / Re: PDB conversion
« on: May 31, 2017, 07:48:45 am »
3DNA does not have a tool to perform such auto coversions. I vaguely remember Babel could do a better job in some cases, from 3DNA users. Check the openbabel community, and let us know what you find.

An the end of th day, only you know your system well. It may be feasible to write a script/program to convert your .XYZ to .PDB efficiently, taking consideration of standard naming convention of the A/C/G/T/U bases.

Xiang-Jun

13
General discussions (Q&As) / Re: PDB conversion
« on: May 29, 2017, 12:05:23 pm »
Hi Kyle,

As shown in the attached image, your PDB file does not have proper atoms naming for the nucleotides. Specifically, atoms in your OpenBabel converted PDB file are simply named C, N, O for base, sugar and the phosphate. A section of your PDB file is listed below.

Code: [Select]
HETATM    1  C   UNK     1       2.399  -4.315  -0.508  1.00  0.00           C
HETATM    2  O   UNK     1       1.582  -4.309   0.656  1.00  0.00           O
HETATM    3  C   UNK     1       2.481  -2.904  -1.056  1.00  0.00           C
HETATM    4  O   UNK     1       1.218  -2.500  -1.603  1.00  0.00           O
HETATM    5  C   UNK     1       2.845  -1.853  -0.001  1.00  0.00           C
HETATM    6  O   UNK     1       3.660  -0.873  -0.641  1.00  0.00           O
HETATM    7  C   UNK     1       1.485  -1.297   0.415  1.00  0.00           C
HETATM    8  C   UNK     1       0.639  -1.443  -0.851  1.00  0.00           C
HETATM    9  N   UNK     1      -4.340  -0.429  -1.822  1.00  0.00           N
HETATM   10  C   UNK     1      -3.213   0.196  -2.239  1.00  0.00           C
HETATM   11  N   UNK     1      -1.952  -0.117  -1.914  1.00  0.00           N
HETATM   12  C   UNK     1      -1.870  -1.170  -1.108  1.00  0.00           C
HETATM   13  C   UNK     1      -2.957  -1.913  -0.612  1.00  0.00           C
HETATM   14  C   UNK     1      -4.215  -1.480  -1.014  1.00  0.00           C
HETATM   15  N   UNK     1      -2.509  -2.950   0.192  1.00  0.00           N
HETATM   16  C   UNK     1      -1.209  -2.829   0.175  1.00  0.00           C
HETATM   17  N   UNK     1      -0.752  -1.767  -0.583  1.00  0.00           N
HETATM   18  P   UNK     1       4.328   0.338   0.255  1.00  0.00           P
HETATM   19  C   UNK     1       2.724   2.003  -0.968  1.00  0.00           C
HETATM   20  O   UNK     1       3.104   1.437   0.279  1.00  0.00           O
HETATM   21  C   UNK     1       1.430   2.759  -0.796  1.00  0.00           C
HETATM   22  O   UNK     1       0.387   1.842  -0.466  1.00  0.00           O
HETATM   23  C   UNK     1       1.426   3.850   0.313  1.00  0.00           C
HETATM   24  O   UNK     1       1.219   5.147  -0.230  1.00  0.00           O
HETATM   25  C   UNK     1       0.209   3.484   1.163  1.00  0.00           C
HETATM   26  C   UNK     1      -0.597   2.602   0.209  1.00  0.00           C
HETATM   27  N   UNK     1      -1.539   1.692   0.839  1.00  0.00           N
HETATM   28  C   UNK     1      -2.880   1.786   0.508  1.00  0.00           C
HETATM   29  O   UNK     1      -3.338   2.618  -0.262  1.00  0.00           O
HETATM   30  N   UNK     1      -3.678   0.857   1.137  1.00  0.00           N

3DNA (and DSSR/SNAP) requires standard names for a nucleotide to be recognized -- see Fig.1 of the 2015 DSSR NAR paper. Check a RCSB PDB entry (see below), e.g., 355d, you will see how the atoms are named:

Code: [Select]
ATOM     17  P    DG A   2      23.337  31.278  21.156  1.00 13.26           P
ATOM     18  OP1  DG A   2      24.761  31.571  21.391  1.00 13.17           O
ATOM     19  OP2  DG A   2      22.651  31.834  19.956  1.00 12.34           O
ATOM     20  O5'  DG A   2      23.180  29.714  21.092  1.00 12.20           O
ATOM     21  C5'  DG A   2      23.830  28.894  22.040  1.00 10.87           C
ATOM     22  C4'  DG A   2      23.663  27.461  21.627  1.00 10.59           C
ATOM     23  O4'  DG A   2      22.328  27.016  21.920  1.00 10.81           O
ATOM     24  C3'  DG A   2      23.866  27.232  20.130  1.00 11.75           C
ATOM     25  O3'  DG A   2      24.412  25.926  20.055  1.00 16.36           O
ATOM     26  C2'  DG A   2      22.447  27.195  19.590  1.00 10.31           C
ATOM     27  C1'  DG A   2      21.722  26.527  20.744  1.00  8.31           C
ATOM     28  N9   DG A   2      20.293  26.737  20.884  1.00  6.86           N
ATOM     29  C8   DG A   2      19.536  27.799  20.464  1.00  7.02           C
ATOM     30  N7   DG A   2      18.276  27.683  20.786  1.00  7.92           N
ATOM     31  C5   DG A   2      18.201  26.464  21.447  1.00  5.72           C
ATOM     32  C6   DG A   2      17.091  25.790  22.018  1.00  5.63           C
ATOM     33  O6   DG A   2      15.916  26.151  22.052  1.00  7.25           O
ATOM     34  N1   DG A   2      17.464  24.566  22.588  1.00  4.99           N
ATOM     35  C2   DG A   2      18.749  24.064  22.600  1.00  4.83           C
ATOM     36  N2   DG A   2      18.930  22.867  23.187  1.00  6.47           N
ATOM     37  N3   DG A   2      19.786  24.688  22.072  1.00  6.26           N
ATOM     38  C4   DG A   2      19.440  25.872  21.516  1.00  6.25           C

HTH,

Xiang-Jun

14
FAQs / How to make the best use of the Forum
« on: May 19, 2017, 11:35:45 am »
  • Register to download the 3DNA software (including DSSR and SNAP) and to post questions. Non-registered viewers can only read existing posts; they will not see the Downloads section and they are not allowed to post on the Forum. Over the years, I've received many private emails asking for help, and those users have been (mostly) responded with the following canned message:

    Quote
    Thanks for your interest in using 3DNA. Please be aware that for the benefit of the 3DNA-user community at large, I do not provide private email support; the 3DNA Forum (http://forum.x3dna.org/) has been created specifically for open discussions of all 3DNA-related issues. In other words, *any* 3DNA-associated questions are welcome and should be directed there. Specifically, please do *not* be shy in sharing openly and concretely difficult experiences you may have in installing or using the software.

    By asking your questions on the public 3DNA Forum, you are not only benefiting yourself but also the user community. I monitor the Forum regularly and always respond to posts promptly. I look forward to 'seeing' you on the 3DNA Forum (http://forum.x3dna.org/).
  • Post on the Forum any 3DNA-related questions, or share your experience/use-case with the community. After registration, you must post your questions yourself on the Forum to get them answered. Specifically, I do not post your questions asked privately via email on the Forum on your behalf.
  • Click the Notify button (in the upper right corner) to receive email alert of new posts in the threads or sections you are interested in. I get notified for each and every new post on the Forum so I can react promptly.
  • Share what you've learned through help from others. Share what you know that could be of interest to the general 3DNA user community. Be helpful.
  • Behave yourself. No spam or trolling allowed. Violators are removed immediately without any further notice.

15
General discussions (Q&As) / Re: Top view of DNA
« on: May 18, 2017, 10:58:19 am »
Hi mary,

Thanks for providing further details. Now I understand what you want to achieve. 

Quote
Does 3DNA correct the orientation of pdb automatically?
No, 3DNA does correct the orientation of pdb automatically.

The stack2img command is intended to be used with the analyze-generated 'stacking.pdb' file, as shown in the example from stack2img -h. It is not a general purpose grogram to set an arbitrary structure in top view. The DNA image (within x3dna_v1.5.pdf) you attached is a fiber model that is already in top view.

If you can find the helical axis, as in the case of 'dne_l.pdb', you could follow recipe #4 ($X3DNA/R4_4way_junction) described in the the 2008 3DNA Nature Protocols paper. Alternatively, you may find blcoview helpful.

You should also look elsewhere (e.g., PyMOL, Chimera, etc) for such functionality.

Xiang-Jun

Pages: [1] 2 3 ... 73

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.