Recent Posts

81

FAQs / How to set up 3DNA on Windows with WSL2

« Last post by nat520 on December 14, 2024, 06:47:13 am »

Dear Dr. Lu,

I am trying to install x3dna-v2.4 on Windows 11 following the instructions.
However, I still can't execute find_pair -h on ConEmu.
I tried to perform some troubleshooting by looking over similar issues posted on this forum, such as "dir", "echo %X3DNA%", "echo %PATH%" and "dir %X3DNA%config\version".. and all the feedbacks seem alright..
I actually have tried Ruby and Mingw too but that all still didn't work out so in the end i got rid of them.
I have attached the screenshots, can you help on this, where have I missed out?
And I would like to get a confirmation that x3dna-v2.4 does not need a license to download, and working on native window using ConEmu is perfectly alright?

Kind Regards,
Chian

82

FAQs / Re: Running DSSR on macOS

« Last post by xiangjun on November 08, 2024, 09:30:04 pm »

As a follow up, please note that:

The CTV distributes DSSR Basic and Pro versions in zip format for macOS, Linux, and Windows. Each zip file contains a DSSR binary executable as well as the associated user manual.

Assuming basic command-line knowledge, users should be able to follow the instructions in the manual and reproduce reported results.

83

FAQs / Re: Running DSSR on macOS

« Last post by xiangjun on November 08, 2024, 06:46:53 pm »

Thanks for your interest in using DSSR. Your screenshot provides information that explains why you're having problems using DSSR.

You're on a macOS, and you have double-clicked the x3dna-dssr executable to run it. I can reproduce your case by installing x3dna-dssr under the ~/Downloads folder and double-clicking it. The error message is quite informative, by showing that x3dna-dssr is run, and immediately exit. Running x3dna-dssr without any options gives the following message:

missing required option: must specify -i=PDBFile/mmCIF

type: 'x3dna-dssr -h (or --help)' for further help
      'x3dna-dssr --citation' for preferred citation(s)

Time used: 00:00:00:00

That means DSSR is already successfully installed on your macOS. It is just that DSSR is a command-line (CLI) program, and you need a terminal window to run it. There are many online tutorials on how to get started using terminal on macOS. Here is one: Absolute BEGINNER Guide to the Mac OS Terminal. Once you are familiar with the terminal, running DSSR should be straightforward, as detailed in the User Manual.

The DSSR executable (x3dna-dssr for macOS and Linux, and x3dna-dssr.exe for Windows) is self-contained and does not rely on any third-party libraries. There is no need for any setup or configurations: type x3dna-dssr -h to verify your installation. Note that DSSR is a command-line program: you need a terminal window to run it.

If you're GUI-driven and do not want to use CLI at all, then you may find the following two resources helpful:

• DSSR-enabled Innovative Schematics of 3D Nucleic Acid Structures with PyMOL
• Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures

Best regards,

Xiang-Jun

84

FAQs / Running DSSR on macOS

« Last post by lillytishkoff on November 08, 2024, 01:36:12 am »

DSSR Download Issue

 received a license approval to download DSSR- Basic and when I downloaded, I received an error. The software is still not working (see screenshot). Please advise how I can fix.

85

RNA structures (DSSR) / Re: plotting the helical axis along curved helices

« Last post by xiangjun on October 25, 2024, 08:46:14 pm »

Hi Di,

Do you have any idea of how to easily find the axis of each 2-bp segment of a helix?

The info is within DSSR, but not exposed. I'm considering to add this feature in DSSR JSON output for easy parsing. For WC-like pairs, things are not that complicated. However, with there are subtitles with non-Watson-Crick pairs, e.g., Hoogsteen and reverse Hoogsteen base pairs.

Also, I think an easier solution for A-form helix is to do a shift of the origin in the plane of the reference frame so that the shifted origin is where the axis passes through the plane.

See "Worked examples on base-pair parameters" in the DSSR Pro User Manual. especially Session "6 Local helical parameters". The vectors o1_h and o2_h are what you need. They are not simple shifts of the origin in the reference frame.

This thread actually prompt me to refine the detailed algorithmic descritpion and get the content published. They are the real meat of 3DNA!

Best regards,

Xiang-Jun

86

RNA structures (DSSR) / Re: plotting the helical axis along curved helices

« Last post by Di_Liu on October 25, 2024, 07:42:23 pm »

Thanks, Xiang-Jun!

Do you have any idea of how to easily find the axis of each 2-bp segment of a helix?

Also, I think an easier solution for A-form helix is to do a shift of the origin in the plane of the reference frame so that the shifted origin is where the axis passes through the plane.

Di

87

RNA structures (DSSR) / Re: plotting the helical axis along curved helices

« Last post by xiangjun on October 24, 2024, 10:53:08 pm »

Hi Di,

Thanks for posting on the Forum. Indeed the origins of base-pairs are centered within a pair, as defined in the standard base reference frame. For B-form DNA where the helical axis passes through and is perpendicular to base pairs, the line connecting bp origins appears as expected. For A-form DNA or RNA (which is in A-form), the helical axis passes through the central hole where the bps (and their origins) spiral around. See "Figure 4. Influence of non‐zero Slide and Roll at sequential dimer steps on overall DNA helical conformation" of the 2003 3DNA paper in NAR.

DSSR does output a linear helical axis when a helical segment is not too strongly curved. See the 2015 DSSR paper "Figure 2 -- analysis of the yeast phenylalanine tRNA (1ehz)" for an example. You could also run the following commands:

Code: [Select]

x3dna-dssr -i=1ehz.pdb --helical-axis
pymol 1ehz.pdb dssr-helicalAxes.pdb
# within PyMOL: as lines; png 1ehz-helices.png
You will see an image as attached below.

However, DSSR currently does not fit a smooth curvilinear helical axis around an arbitrary shape, e.g., a DNA circle. In principle, DSSR can fit a mini-helical axis for each base-pair step (i.e., a 2-bp segment) and then perform a b-spline interpolation. I'm open to suggestions and welcome collaborations to pursue this topic further.

Best regards,

Xiang-Jun

88

RNA structures (DSSR) / plotting the helical axis along curved helices

« Last post by Di_Liu on October 24, 2024, 07:45:43 pm »

Hi Xiang-Jun,

I tried to extract the coordinates of the origin points of the base-pair reference frame from the json file. It appears working for DNA structures; but for RNA, the points form a spiral around the helical axis (see attached image), as we would expect due to the differences of how the axis passes through the base-pairs in B- and A-form helices.

Thanks,

Di

89

Site announcements / X3DNA-DSSR is funded and DSSR Basic is free for academic users

« Last post by xiangjun on September 25, 2024, 10:31:18 am »

Dear 3DNA/DSSR users,

It gives me great pleasure to announce that the 3DNA/DSSR project is now funded by the NIH R24GM153869 grant, "X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids". I am deeply grateful for the opportunity to continue working on a project that has basically defined who I am. It was a tough time during the funding gap over the past few years. Nevertheless, I have experienced and learned a lot, and witnessed miracles enabled by enthusiastic users.

Since late 2020 when I lost my R01 grant, DSSR has been licensed by the Columbia Technology Ventures (CTV). I appreciate the numerous users (including big pharma) who purchased a DSSR Pro License or a DSSR Basic paid License. Thanks to the NIH R24GM153869 grant, we are pleased to provide DSSR Basic free of charge to the academic community. Academic Users may submit a license request for DSSR Basic or DSSR Pro by clicking "Express Licensing" on the CTV landing page. Commercial users may inquire about pricing and licensing terms by emailing techtransfer@columbia.edu, copying xiangjun@x3dna.org.

The current version of DSSR is v2.4.5-2024sep24 which contains miscellaneous bug fixes (e.g., chain id with > 4 chars) and minor improvements. This release synchronizes with the new R24 funding, which will bring the project to the next stage. All existing users are encouraged to upgrade their installation.

Lots of exciting things will happen for the project. The first important thing is to make DSSR freely accessible to the academic community. I'm now starting to monitor the Forum closely and answer users questions promptly.

I am committed to making DSSR a brand that stands for quality and value. By virtue of its unmatched functionality, usability, and support, DSSR saves users a substantial amount of time and effort when compared to other options. My track record throughout the years has unambiguously demonstrated my dedication to this solid software product.

Xiang-Jun

DSSR Basic contains all features described in the three DSSR-related papers, and include the originally separate SNAP program (still unpublished) for analyzing DNA/RNA-protein complexes. The Pro version integrates the classic 3DNA functionality, plus advanced modeling routines, with email/Zoom/phone support.

90

RNA structures (DSSR) / Re: How the length of the sequence depends on _pdbx_unobs_or_zero_occ_atoms ???

« Last post by sk on September 06, 2024, 10:23:46 am »

Thank you, Xiang-Jun.