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1
Site announcements / DSSR-enhanced visualization of nucleic acid structures in PyMOL
« Last post by xiangjun on December 02, 2019, 12:33:46 pm »
This website http://skmatic.x3dna.org/ (see screenshot below) aims to showcase DSSR-enabled cartoon-block schematics of nucleic acid structures using PyMOL. It presents a simple interface to browse pre-calculated PDB entries with a set of default settings: long rectangular blocks for Watson-Crick base-pairs, square blocks for G-tetrads in G-quadruplexes, with minor-groove edges in black. Users can also specify an URL to a PDB- or mmCIF-formatted file or upload such an atomic coordinates file directly, and set several common options to customerize to the rendered image.

Moreover, a web API to DSSR-PyMOL schematics is available to allow for its easy integration into third-party tools.


Input a PDB id
Pre-calculated cartoon-block images together with summary information are available for PDB entries of nucleic-acid-containing structures. Note that gigantic structures like ribosomes that are only represented in mmCIF format are excluded from the resource. The base block images are most effective for small to medium-sized structures.

Here are a few examples:
  • 1ehz, the crystal structure of yeast phenylalanine trna at 1.93-A resolution
  • 2lx1, the major conformation of the internal loop 5'GAGU/3'UGAG
  • 2grb, the crystal structure of an RNA quadruplex containing inosine-tetrad
  • 4da3, the crystal structure of an intramolecular human telomeric DNA G-quadruplex 21-mer bound by the naphthalene diimide compound MM41
  • 1oct, crystal structure of the Oct-1 POU domain bound to an octamer site
  • 2hoj, the crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ions

Each entry is shown with images in six orthogonal perspectives: front, back, right, left, top, bottom. The 'front' image (upper-left in the panel) is oriented into the most-extended view with the DSSR --blocview option. The corresponding PyMOL session file and PDB coordinate file are available for download. One can also visualize the structure interactively via 3Dmol.js.

Sample PDB entries
Users can browse random samples of pre-calculated PDB entries. The number should be between 3 and 99, with a default of 12 entries (see below for an example). Simply click the 'Submit' button or the link "Random samples (3 to 99)" to see random results of 12 entries each time.

Specify an coordinate file
The atomic coordinate file must be in PDB or mmCIF format, and can be optionally gzipped (.gz). One can either specify an URL to or select a coordinate file. Several common options are available to allow for user customizations.

Web API help message
Usage with 'http' (HTTPie):
    http -f http://skmatic.x3dna.org/api [options] url=|model@
    http http://skmatic.x3dna.org/api/pdb/pdb_id  -- for a pre-calculated PDB entry
    http http://skmatic.x3dna.org/api/help        -- display this help message
Options:
    block_file=styles-in-free-text-format [e.g., block_file=wc-minor]
    block_color=nt-selection-and-color    [e.g., block_color='A:pink']
    block_depth=thickness-of-base-block   [e.g., block_depth=1.2]
    r3d_file=true-or-FALSE(default)       [e.g., r3d_file=true]
    raw_xyz=true-or-FALSE(default)        [e.g., raw_xyz=true]
Required parameter
    url=URL-to-coordinate-file [e.g., url=https://files.rcsb.org/download/1ehz.pdb.gz]
    model@coordinate-file      [e.g., model@1ehz.cif]
    # Only one must be specified. 'url' precedes 'model' when both are specified.
    # The coordinate file must be in PDB or PDBx/mmCIF format, optionally gzipped.
Examples
    http -f http://skmatic.x3dna.org/api block_file='wc-minor' model@1ehz.cif r3d_file=t
    http -f http://skmatic.x3dna.org/api url=https://files.rcsb.org/download/1ehz.pdb.gz -d -o 1ehz.png
    http http://skmatic.x3dna.org/api/pdb/1ehz -d -o 1ehz.png
    # with 'curl'
    curl http://skmatic.x3dna.org/api -F 'model=@1msy.pdb' -F 'block_file=wc-minor' -F 'r3d_file=1'
    curl http://skmatic.x3dna.org/api -F 'url=https://files.rcsb.org/download/1ehz.pdb.gz' -o 1ehz.png
    curl http://skmatic.x3dna.org/api/pdb/1ehz -o 1ehz.png

 
Sample images
       
2
General discussions (Q&As) / Re: Where and How do I enter a Base Pair Sequence?
« Last post by xiangjun on November 21, 2019, 02:11:34 pm »
Quote
Where do I enter a nucleotide base pair sequence? How do I enter a nucleotide base pair sequence? Like this: ATCGAAGGTC? or like this: A/T/T/C/G/? May I please have a link?

It is not clear (to me at least) what you mean by entering "a nucleotide base pair sequence", without contextual information. In 3DNA, the fiber command allow you to specify a specific base sequence for generic A-, B-, and C-DNA models. Run "fiber -h" for details.

In the Web 3DNA 2.0 website, see the http://web.x3dna.org/index.php/fibermodel section (the top 5 models) for examples.

Best regards,

Xiang-Jun
 

3
General discussions (Q&As) / Where and How do I enter a Base Pair Sequence?
« Last post by AlanWhite on November 21, 2019, 02:03:49 pm »
Where do I enter a nucleotide base pair sequence? How do I enter a nucleotide base pair sequence? Like this: ATCGAAGGTC? or like this: A/T/T/C/G/? May I please have a link?   
4
Quote
It worked with do_x3dna VMD plugin.

I do not know if it works now. For any do_x3dna specific questions, please ask the authors/developers directly. I was not involved in that project and I cannot provide any practical help for do_x3dna.

Best regards,

Xiang-Jun
5
Dear Prof. xiangjun, thanks for your suggestion. It worked with do_x3dna VMD plugin.

Thanks,
Tanashree
6
Quote
I tried with the changes you suggested and it worked.

Glad to hear that the suggested method works. Thanks for the update.

Quote
Now another doubt is I have to run these calculations for multiple PDB files at a time. I guess analyze option is overwriting the file names wehn I am trying to run in for loop and I could not find any option to give the output file name after analyze command.

Since you are running 'analyze' in a loop to process multiple PDB files, you should be able to rename the default output file as desired. Without further details, that's all I could say.

Best regards,

Xiang-Jun
7
Thanks, Prof. xiangjun for your prompt reply. I tried with the changes you suggested and it worked. The modified base was considered as t. Now another doubt is I have to run these calculations for multiple PDB files at a time. I guess analyze option is overwriting the file names wehn I am trying to run in for loop and I could not find any option to give the output file name after analyze command. 

Thanks,
Tanashree
8
Hi Tanashreee,

Thanks for using 3DNA and for posting your questions on the Forum.

Quote
I added the name in baselist.dat I am using 2.0 version.  Also, I kept the Atomic_TG.PDB file in config folder as shown for 5MC modification.  When I tried to analyze program is analyzing just for the 10 base pairs and not all 13.

Please upgrade to 3DNA v2.4, which detects 12 base-pairs out of the expected 13. Version 2.0 is more than 10 years old, and there is no practical reasons to use it anymore.

3DNA does not detect the ADE-TG pair due to improper labeling of base atoms in the modified TG. See the attached image of the pair, and pay close attention to the TG base ring (e.g., C7 connects to N1 etc.)

Rectify names of the TG base atoms following PDB convention (as for T), 3DNA should then work. Please have a try and report back how it goes.

Best regards,

Xiang-Jun




9
I want to analyze the base-pair parameters of 13 mer DNA double helix. I have one modified base Thymine Glycol in my strand.

I added the name in baselist.dat I am using 2.0 version.  Also, I kept the Atomic_TG.PDB file in config folder as shown for 5MC modification.  When I tried to analyze program is analyzing just for the 10 base pairs and not all 13.

I am attaching DNA duplex file and separate modified base file and also the .dat file in config folder

Thanks & Regards,
Tanashreee
10
DNA/RNA-protein interactions (SNAP) / Re: About sugar-pi stacking
« Last post by xiangjun on November 08, 2019, 04:27:51 pm »
Hi Honglue,

Have you found a solution to your sugar-pi stacking task? If so, you are encouraged to share your findings with the 3DNA Forum community. If you have not found a practical solution yet and you are still interested in this topic, I may consider to add this feature to SNAP.

Best regards,

Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.