Messages

151

RNA structures (DSSR) / Re: nt_ids for residues i+1 and i-1

« on: February 19, 2021, 11:01:07 am »

Hi Brinda,

Thanks for your request for a new feature in DSSR. Without funding support, I am not able to devote time/effort to new features to DSSR Basic other than bug fixes. Further development and user support are thus being committed to DSSR Pro version only.

Best regards,

Xiang-Jun
 

152

RNA structures (DSSR) / Re: 3DNA-DSSR

« on: February 19, 2021, 12:26:56 am »

In addition to my previous response, and just to clarify: Since August 2020 when DSSR became formally licensed, well over a hundred DSSR licenses have been issued via the CTV website. On average, that is approximately one license per week-day, to a total of 106 organizations world wide. As far as I know, all legitimate registrations have been promptly processed, thanks to the time/effort from the CTV support staff.

Xiang-Jun

153

RNA structures (DSSR) / Re: 3DNA-DSSR

« on: February 18, 2021, 11:09:43 pm »

Hi,

DSSR is available exclusively via the CTV website. Note that "DSSR Pro includes an in-depth user manual, and one year technical support directly from the developer. DSSR basic is provided AS IS, and does not include any support."

The Download instructions post has the following explicit information:

DSSR v2.2 has been released, with SNAP integrated into it. The stand-alone x3dna-snap program is gone and its functionality has been replaced by x3dna-dssr snap. Here is an overview of DSSR. DSSR has superseded 3DNA v2.4, with vastly expanded features and dramatically improved usability. Please visit the Columbia Technology Ventures (CTV) website to obtain a license and to download DSSR.

Hopefully, the message is simple and clear enough.

Xiang-Jun

154

w3DNA -- web interface to 3DNA / MOVED: composite DNA template length

« on: February 18, 2021, 11:09:00 am »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=952.0

155

General discussions (Q&As) / MOVED: Extending DNA in protein-DNA complex - issue with final steps

« on: February 18, 2021, 11:07:23 am »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=954.0

156

General discussions (Q&As) / MOVED: Circular DNA parameters

« on: February 18, 2021, 11:07:07 am »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=939.0

157

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

« on: February 17, 2021, 03:20:04 pm »

Hi,

Sorry to hear your trouble in downloading DSSR from the CTV website. Did you notice the "Express Licensing" tab at the top?

Over the past six months or so, the CTV has issued numerous DSSR licenses to users worldwide, mostly in academia. So obtaining DSSR is no longer a problem. At the beginning, some users got confused of registration on the 3DNA Forum to download 3DNA v2.4 and asking questions, and licensing of DSSR from the CTV.

Best regards,

Xiang-Jun

158

RNA structures (DSSR) / Re: Circular DNA parameters

« on: February 16, 2021, 08:56:51 pm »

As a follow-up, DSSR Pro now has modeling features that can produce circular DNAs and DNA super helices as shown below.

Best regards,

Xiang-Jun

159

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

« on: February 11, 2021, 04:46:42 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. Using your 1kx5 as an example, one can easily build the attached model. See also two more complexes models.

This novel modeling program is distributed as a module of DSSR Pro.

Best regards,

Xiang-Jun

160

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

161

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

162

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

163

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

164

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

 

165

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

166

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

167

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

168

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

169

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

170

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

171

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

172

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

173

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

174

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

175

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.