Messages

101

w3DNA -- web interface to 3DNA / Re: Binding site orientation in Composite

« on: February 11, 2021, 04:34:22 pm »

Hi,

I have created a brand-new program for template-based modeling of nucleic acid structures, including DNA-protein complexes. Now users can easily specify their own templates, as well as their orientations, via the command-line. This novel modeling program is distributed as a module of DSSR Pro.

Best regards,

Xiang-Jun

102

w3DNA -- web interface to 3DNA / Re: Composite

« on: February 11, 2021, 04:33:40 pm »

Hi,

I have created a brand-new program for template-based modeling of nucleic acid structures, including DNA-protein complexes. Now users can easily specify their own templates via the command-line. This novel modeling program is distributed as a module of DSSR Pro.

Best regards,

Xiang-Jun

103

RNA structures (DSSR) / Re: Extending DNA in protein-DNA complex - issue with final steps

« on: February 11, 2021, 04:28:33 pm »

Thanks for letting us know that you have now solved your problem on extending DNA at both ends in a DNA-protein complex. Template-based model building of DNA-protein complexes is a persistent issue, as demonstrated in this thread, the one you referred to, and the most recent questions on the Composite module of Web 3DNA 2.0. The traditional 3DNA-based approach 'works', but it is tedious and error prone. The process is technically challenging for non-expert 3DNA users. There are also certain inherent limitations in the approach, as you experienced.

I have created a brand-new program for template-based modeling of nucleic acid structures, including DNA-protein complexes. Using your example, extending 4wlw on 5'-end by fiber B-DNA duplex TTG and 3'-end by CTAACCT can be easily achieved. It literally takes only a couple of minutes. See the attached PDB coordinate file and a schematic image. This novel modeling program is distributed as a module of DSSR Pro.

Best regards,

Xiang-Jun

104

RNA structures (DSSR) / Re: Extending DNA in protein-DNA complex - issue with final steps

« on: February 03, 2021, 03:55:02 pm »

Hi,

Glad to know that you have figured out the issues. Instead of deleting your posts, could you please provide step-by-step procedure on how you solved the problem for the benefit of other users? The summary could also serve as a future reference for yourself.

Best regards,

Xiang-Jun

105

RNA structures (DSSR) / Re: composite DNA template length

« on: January 21, 2021, 09:46:41 pm »

Hi,

Thanks for your question on the Composite module in Web 3DNA 2.0. Composite is an advanced feature that mades use various 3DNA programs and ad hoc scripts. Other than the general idea, I honestly do not know how things work in details. Right now, I have no time to dig things up either. In the long run, I may consider to consolidate all these steps into a DSSR module to automate the process.

Shuxiang, the developer of Web 3DNA 2.0 but no longer involved in the project, may chime in with some insights.

Xiang-Jun

 

106

RNA structures (DSSR) / Re: x3dna-dssr -h no response

« on: January 15, 2021, 09:53:57 pm »

Hi,

• The 3DNA suite of programs (up to v2.4) has been superseded by DSSR. See the Overview PDF, especially Section 1.4 DSSR vs. 3DNA vs. SCHNAaP/SCHNArP.
• DSSR is licensed by Columbia University. It is available only through the website http://innovation.columbia.edu/technologies/CU20391
• 3DNA v2.4 (along with SCHNAaP/SCHNArP) is still available for downloaded from this Forum, but it is on longer developed/supported.

Hope this helps.

Xiang-Jun

107

RNA structures (DSSR) / Re: DSSR eta-base theta-base

« on: January 09, 2021, 07:19:44 pm »

Hi Cathy,

Happy 2021!

Following your request, I've updated DSSR so that the JSON output for pseudo-torsion angles eta_base and theta_base would be "null" instead of 0.0 when they cannot be calculated. I have also refined DSSR to account for chain breaks while calculating all pseudo torsions.

The updated DSSR (v2.2.1) will be available from the Columbia Technology Ventures (CTV) website, presumably by early next week. As you may know, DSSR is now licensed by Columbia University.

Best regards,

Xiang-Jun

108

General discussions (Q&As) / Re: How 3DNA calculate base overlapping?

« on: December 27, 2020, 02:28:29 pm »

Please read the 2003 3DNA paper and the 2015 DSSR paper.

Xiang-Jun

109

DNA/RNA-protein interactions (SNAP) / Re: How to download the SNAP code?

« on: December 27, 2020, 02:25:50 pm »

A quick note: SNAP has been integrated into DSSR, as of v2.2, and available for download from CTV.

Xiang-Jun

110

FAQs / Re: Where to download x3DNA

« on: December 08, 2020, 05:34:07 pm »

Hi Pawel,

You should now be able to see the Download section.

There is a lag from the time an account is activated to it being granted download access. The rules for registration/download have been tightening up to keep the Forum spam free, and to serve legitimate users only. I have updated the FAQ entry "How to make the best use of the Forum" to make the process more transparent.

Best regards,

Xiang-Jun

111

DNA/RNA-protein interactions (SNAP) / Re: Difference between pi-stacking and pi-pair in SNAP

« on: December 07, 2020, 12:33:28 pm »

The base/amino-acid pairs identified by SNAP are named pseudo pairs (see doi: 10.1093/nar/gkr452). I have never heard of the term "pi-pair" as used in the your initial message. So I was confused as to what it really means.

Using 1oct as an example, a graphical illustration of the A-gln pseudo-pair (A.DA204 and C.GLN44) is attached. It should be clear that it is indeed like a base pair (H-bonds, coplanar).

Please generate a similar graph of a base/amino-acid stacking interaction and post it back. This way you would better understand the differences between the DSSR output sections on pair vs stack. It also helps other viewers of the thread.

Best regards,

Xiang-Jun

112

DNA/RNA-protein interactions (SNAP) / Re: Difference between pi-stacking and pi-pair in SNAP

« on: December 07, 2020, 08:01:08 am »

Hi Takayuki Kimura,

Please clarify your question by providing concrete examples of "pi-stack and pi-pair" in relation to SNAP output.

Thanks,

Xiang-Jun

113

DNA/RNA-protein interactions (SNAP) / Re: How to download the SNAP code?

« on: November 19, 2020, 01:57:12 pm »

SNAP can be downloaded from the "Downloads/3DNA download" Section of the 3DNA Forum.

Xiang-Jun

114

RNA structures (DSSR) / Re: 3DNA/DSSR download issue

« on: November 18, 2020, 11:19:09 am »

Hi,

You should be able to see the "Downloads" section now.

As of v2.0, DSSR is licensed by Columbia University, and it is only available from the Columbia Technology Ventures (CTV) website.

Best regards,

Xiang-Jun

115

FAQs / Re: license missing in x3dna-v2.4 file (window version)

« on: November 11, 2020, 03:13:00 pm »

Hi Jianhui,

Thanks for your enquiry about 'missing' the 3DNA-v2.4 license file. There is a long and complicated history regarding the 3DNA software and its licensing. Basically, the 3DNA-v2.4 software package is free for academic use, even though no license file is explicitly distributed with the  tarball.

DSSR 2.0, which has completely replaced 3DNA v2.x, has been formally licensed by Columbia University. See the overview PDF: http://docs.x3dna.org/dssr2-overview.pdf.

3DNA 2.x is no longer supported for 'free' as it used to be for the past decade. A paid DSSR license from Columbia is required for future technical support.

Best regards,

Xiang-Jun

116

MD simulations / Re: Superimpose representative cluster of a RNA strand after simulation

« on: November 10, 2020, 06:55:08 pm »

Hi,

Please provide concrete examples to illustrate unambiguously what you what to achieve.

Best regards,

Xiang-Jun

PS. DSSR 2.x (paid version) contains built-in support for the analysis of MD simulations, and advanced features for DNA/RNA modeling. It can also be used to perform sequence-independent search/fitting employing base as well as backbone structures.

117

RNA structures (DSSR) / Re: wDSSR showing invalid ID on a valid PDB ID

« on: November 07, 2020, 09:31:40 am »

Sorry -- wDSSR is no longer supported, as least for now.

If users find 3DNA/DSSR useful and continued support for the project indispensable, you are welcome to make your case/thought publicly in the Forum or sending me email.

See also my response to http://forum.x3dna.org/general-discussions/circular-dna-parameters/.

Xiang-Jun

118

RNA structures (DSSR) / Re: Circular DNA parameters

« on: October 30, 2020, 03:46:34 pm »

Dear Thor,

Thanks for your insightful questions on building perfectly circular DNAs of various sizes. DNA/RNA modeling is a topic of great significance and there is clearly a lack of practical software tools. I'm interested in developing new modeling features in DSSR, a replacement of the classic 3DNA suite of programs. Nevertheless ...

Thank you for developing (and maintaining) this collection of beautiful and practical DNA geometry software!

I've enjoyed maintaining 3DNA for nearly two decades. With NIH funding support over the past 9 years, I created DSSR as a replacement of 3DNA v2.x. Alas, I am now out of luck to continuously serve the community for free via NIH funding support, as it used to be.

DSSR is now licensed by Columbia University. Please buy a license if users find 3DNA/DSSR useful and my service valuable. Think in terms of the time/efforts you would otherwise have to spend. Further support and development of DSSR (including customized applications) will be devoted to paid users only -- that's the new normal.

Best regards,

Xiang-Jun

119

General discussions (Q&As) / Re: blocview.pl

« on: September 30, 2020, 10:25:32 pm »

Within the 3DNA v2.4 distribution, the original Perl blocview script has been removed to avoid conflict with the Ruby script with the same name. The Ruby blocview script is the one to be used within 3DNA v2.0. Since you asked for the long outdated Perl script (no longer supported), I have dug it out -- see the attached file blocview.pl.

Note that DSSR 2.0 has replaced 3DNA v2.4. Specifically, the DSSR --blocview option has completely superseded the functionality of the Ruby blocview script in 3DNA v2.4, plus more advanced features. See the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" and http://skmatic.x3dna.org.

Best regards,

Xiang-Jun

120

General discussions (Q&As) / Re: changing some of the RNA sequence of an chain to DNA

« on: September 28, 2020, 11:10:37 am »

Hi,

Thanks for your followup -- it helps clarify previous ambiguities.

In 3DNA, you could perform base mutations without changing backbone geometry using the mutate_bases program. As an example, to mutate U6 to DT, you can do the following:

Code: [Select]

mutate_bases 'chain=A snum=6 m=DT' rna2.pdb mutated-U6DT.pdb
You may mutate all four bases simultaneously. Check mutate_bases -h. You then need to remove O2' atoms manually.

DSSR 2.0 has a much powerful modeling module that supersedes mutate_bases, with many more features.

HTH,

Xiang-Jun

121

General discussions (Q&As) / Re: changing some of the RNA sequence of an chain to DNA

« on: September 27, 2020, 05:18:15 pm »

Please be specific: provide an example so that others can reproduce.

As a reminder, here is a list of items in the "Registration Agreement":

When posting on the Forum, please abide by the following rules:

0.  Do your homework; read the FAQ and browse the Forum.
1.  Ask your questions on the *public* 3DNA Forum instead of sending
        xiangjun emails or personal messages. Additionally, please note
        that your posts on the 3DNA Forum are in the *public domain*.
2.  Be specific with your questions; provide a minimal, reproducible
        example if possible; use attachments where appropriate.
3.  Respond to requests for clarification. Failure to do so may result in
        delay or no answer to your questions.
4.  Summarize the solution to your problem from a user's perspective
        by providing step-by-step details, for the community's benefit.
5+ Contribute back to the 3DNA project:
        o Report bugs — including typos
        o Make constructive suggestions — anything that can make 3DNA better
        o Answer other users' questions
        o Share your use cases in the "Users' contributions" section

Xiang-Jun

122

MD simulations / Re: Failed Downloading MD Ruby Scripts of 3DNA

« on: September 16, 2020, 10:38:01 am »

Hi Moi,

Thanks for sharing your way of applying DSSR to the analysis of MD trajectories. The protocol you described is exactly a DSSR user-case I have in mind. DSSR is not targeted specially for MD simulations, for sure. Yet, DSSR fits pragmatically in most situations involving DNA/RNA structural bioinformatics, by design. The MD community will realize the simplicity and applicability of DSSR: it is just a timing issue (when, but not if).

Meanwhile, I notice that, when numbering the stems, I guess the program number the stems by their residue number (from 5' to 3'), namely, the helix with smaller resid at 5' side will be numbered first... Is this correct?

Yes. Try DSSR on 1ehz or other examples you are sure of to check this out.

Xiang-Jun

123

RNA structures (DSSR) / Re: Do you provide DSSR 1.* downloads ?

« on: September 15, 2020, 09:39:25 am »

Hi Louis,

Thanks for your inquires on the DSSR 2.0 release and the CTV licensing.

Only the latest DSSR is maintained to make the long-term support of the software simple and sustainable. DSSR 2.0 (and future releases) should be backward compatible: the main new features of DSSR 2.0 are the modeling modules and the professional manual. All DSSR-related issues should be reported on the open 3DNA Forum, unless a support agreement is arranged otherwise.

I have recently received quite a few enquires about the licensing terms on distributing DSSR as part of a pipeline or in a web service/server. CTV is woking on a policy on such usages. Please ask the CTV for an update on DSSR 2.0 licensing.

Best regards,

Xiang-Jun

124

RNA structures (DSSR) / Re: How to detect very distorted base pair?

« on: September 13, 2020, 01:34:34 pm »

Hi Honglue,

By default, DSSR does not detect these two base pairs because it fails to identify any H-bond between corresponding bases in each pair. These are the cases where users need pay attention to.

For your own understanding and the benefit of other users, it helps that you create an image for each of these base pairs, marking the distances between presumably H-bonded atoms.

Best regards,

Xiang-Jun

125

MD simulations / Re: Unnatural base pair helical parameters

« on: September 10, 2020, 08:18:18 am »

Hi Shaikh,

Can we apply this method to gromacs trajectory or amber trajectory. Or can we use multiple pdb frames to calculate helical parameters.

Follow my previous response, you should be able to find the answers to these questions. For your own understanding and the benefit of other viewers, please post back what you find.

Best regards,

Xiang-Jun