Messages

151

RNA structures (DSSR) / Re: Bug or feature (?) : residue numbering not understood

« on: May 27, 2021, 10:01:18 am »

Hi Louis,

Sorry for your difficult experience in accessing the CTV website for DSSR. I've communicated with the supporting staffs, and hopefully situation would improve as a result of your feedback.

Basically, the DSSR Pro academic license charges a one-time fee of $1000 per seat. It comes with a one-year support directly from me. I do not expect another major release of DSSR in the next 4 years. As a result, the annual cost averages $250, or about a tenth of the cost of a journal publication or a two-night hotel stay. Email and video meetings are included in the one-year support. Following your suggestion, I will create a post on DSSR Pro academic license in the "Site announcements" section. [Note added on May 31, 2021: I've added a post titled "Clarification on DSSR licensing".]

Best regards,

Xiang-Jun

Below in the copied from the CTV website on DSSR Pro:

License Name

DSSR-Pro Academic ($1000, 1 seat)

Description

This academic license is for one user and includes the DSSR Pro software (macOS, linux, and windows) along with the Pro Manual. It is for people working on open academic research at, or for, an academic institution or similar non-profit. Any commercial use requires purchase of a commercial license. It is a one-time fee and does not cover future major releases of the code. Minor releases with bug-fixes and small updates are included in the fee. Thank you for purchasing DSSR. Funds help to support further development of the DSSR software product.

DSSR Pro has more functionality than DSSR Basic, including: (i) homology modeling via in silico base mutations, (ii) easy generation of regular helical models, and (iii) creation of customized structures with user-specific base sequences and rigid-body parameters. DSSR Pro supersedes 3DNA completely while DSSR basic has no modeling capabilities and less analysis/annotation features. DSSR Pro integrates disparate analysis and modeling programs of 3DNA under one umbrella, and offers an easier to use interface. 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.

Pricing Information

Total Price $1,000.00

152

RNA structures (DSSR) / Re: Incorrect topology assignment

« on: May 26, 2021, 11:26:18 pm »

It is possible that there are more mistakes. I am curious what they come
from and I am looking forward to the revised version of the database.

As another concrete example, what do you think the descriptor for PDB entry 6r9k should be?

Xiang-Jun

153

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: May 26, 2021, 06:06:18 pm »

Please provide reproducible examples, illustrated with screenshots if necessary. Otherwise, I (maybe many other viewers of the thread) cannot understand exactly what you are talking about.

154

RNA structures (DSSR) / Re: Color each block nucleotide at each locations

« on: May 26, 2021, 04:18:58 pm »

No, at least not automatically. That said, you could manually select each nucleotide and then color it whatever way you want.

155

General discussions (Q&As) / MOVED: Color each block nucleotide at each locations

« on: May 26, 2021, 04:16:46 pm »

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

http://forum.x3dna.org/index.php?topic=973.0

156

RNA structures (DSSR) / Re: Bug or feature (?) : residue numbering not understood

« on: May 26, 2021, 02:14:06 pm »

Hi Louis,

The issue has been fixed and will be released in DSSR Pro. Due to a lack of funding support, this is the only way my effort on DSSR can be justified. I will ensure that paid users always receive top-notch support.

Xiang-Jun

157

RNA structures (DSSR) / Re: Bug or feature (?) : residue numbering not understood

« on: May 26, 2021, 12:58:58 pm »

Hi Louis,

Thanks for using DSSR and for posting your questions on the 3DNA Forum. I will look into the reported "issue" and get back to you on the Forum, hopefully before long...

Best regards,

Xiang-Jun

158

RNA structures (DSSR) / Re: Incorrect topology assignment

« on: May 26, 2021, 11:17:20 am »

Hi kogucior,

Thanks for using DSSR-G4DB, and for reporting potential issues of the resource on the 3DNA Forum.

I understand what you mean, and DSSR is performing as designed for this case, even though the underlying convention may be changed via an option. You're right that the "inconsistency" is due to the first G-tetrad. Specifically, it is because of the first G, A.DG2, which is in syn instead of anti conformation. There are solid reasons why DSSR is behaving the way it does, one of which being consistent and systematic, instead of ad hoc.

The ordering of four G's in the first G-tetrad in such cases in a deliberate decision. The clockwise (+) and anti-clockwise (-) directionality of the loops, however, can be revised to reflect the progression of the backbone. Your reported case is a good example and will be taken into consideration in the next major release of the DSSR-G4DB resource.

It is possible that there are more mistakes.

As long the first G is in syn conformation, you will observe the same behavior for other G4 structures in DSSR-G4DB. The results should be self-consistent.

I do not have any papers published on G4 yet. The case here is one point of discussion in a manuscript I am working on.

Best regards,

Xiang-Jun

159

RNA structures (DSSR) / Re: Stacking interactions in G-quadruplexes

« on: May 21, 2021, 11:58:26 am »

Hi zw Han,

Please start a new thread when the topic changes. For example, the topic on "the pi-pi stacking interactions between nucleotides in the G-quadruplex structure" is clearly distinct from "The definition of glycoside conformation of guanine nucleotide in nucleic acid". Thus, I've split the original thread into two.

3DNA does not have much to offer on G-quadruplexes, but DSSR does as highlighted in the video overview. So far, I've not published any DSSR paper on G-quadruplexes yet, but already offered some resources. User support, however, is only available to DSSR Pro users.

Best regards,

Xiang-Jun

160

General discussions (Q&As) / MOVED: Stacking interactions in G-quadruplexes

« on: May 21, 2021, 11:48:32 am »

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

http://forum.x3dna.org/index.php?topic=969.0

161

General discussions (Q&As) / Re: The definition of glycoside conformation of guanine nucleotide in nucleic acid

« on: May 20, 2021, 10:26:25 am »

However, there is another new question. That is how to define the glycosidic torsions in the DSSR or 3DNA. Could you please give me a answer?

See my previous response.

Xiang-Jun

162

General discussions (Q&As) / Re: The definition of glycoside conformation of guanine nucleotide in nucleic acid

« on: May 19, 2021, 09:24:28 am »

Hi,

The definition of the glycosidic bond and the corresponding chi (χ) torsion angle which characterizes the relative base/sugar orientation is unambiguous: O4′-C1′-N1-C2 for pyrimidines (C, T and U), and O4′-C1′-N9-C4 for purines (A and G). However, there are different conventions in literature about anti and syn conformations. In addition to Neidle's definition you mentioned, please also see:

• http://jenalib.leibniz-fli.de/ImgLibDoc/nana/chi.gif
• Sokoloski et al. (2011): "Prevalence of syn nucleobases in the active sites of functional RNAs" (https://dx.doi.org/10.1261%2Frna.2759911)
• Dvorkin et al. (2018): "Encoding canonical DNA quadruplex structure" (https://advances.sciencemag.org/content/4/8/eaat3007)

As many other things, a simple concept in principle could be mess in practice. To really get the bottom of it, you could perform a survey of high-resolution, representative DNA/RNA structures in the PDB to see what you get.

HTH,

Xiang-Jun

163

RNA structures (DSSR) / Re: error in rebuild command

« on: May 05, 2021, 04:40:38 pm »

Hi Amir,

3DNA has been completely superseded by DSSR. Due to a lack of funding support, I can no longer devote any effort on 3DNA.

DSSR Pro is the only software product I support right now. A video overview of DSSR is available at: http://docs.x3dna.org/dssr-overview/

Best regards,

Xiang-Jun

164

Site announcements / Video: an overview of DSSR

« on: May 01, 2021, 01:32:37 pm »

I've just released a video "An overview of DSSR" -- http://docs.x3dna.org/dssr-overview/.

DSSR already has a large user base. Based on my observation, however, DSSR is still heavily underused for what it has to offer. This DSSR overview video is for new DSSR users, as well as existing ones.

As always, I appreciate your feedback.

Best regards,

Xiang-Jun

165

FAQs / MOVED: X3DNA and cif

« on: April 30, 2021, 10:45:41 am »

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

http://forum.x3dna.org/index.php?topic=964.0

166

RNA structures (DSSR) / Re: X3DNA and cif

« on: April 30, 2021, 10:30:53 am »

Hi,

3DNA has been completely superseded by DSSR (Pro) which handles PDBx/mmCIF format. 3DNA is the past and no longer supported.

See the video overview of DSSR.

Best regards,

Xiang-Jun

167

FAQs / Re: Where to download x3DNA

« on: April 27, 2021, 09:44:13 pm »

Hi,

You've been granted access to the Download page.

Best regards,

Xiang-Jun

168

RNA structures (DSSR) / Re: License issue of DSSR

« on: April 26, 2021, 09:37:13 am »

Hi Weiwei,

DSSR downloading from CTV should work again now. Please have a try and let us know how it goes.

Best regards,

Xiang-Jun

169

RNA structures (DSSR) / Re: License issue of DSSR

« on: April 22, 2021, 09:59:21 am »

Hi Warren,

Thanks for reporting the DSSR downloading issue from CTV. Here is what I heard from them:

ResoluteAI has stopped working, isn’t allowing us to fix it, and we are working on an alternative. I will be in touch with a timeline as soon as I have one. Apologies, I know this is a big issue and it’s my top priority to fix.

I will post back when the issue is resolved.

Best regards,

Xiang-Jun

170

w3DNA -- web interface to 3DNA / Re: Is there a time lag between PDB deposits and 'Analysis' use?

« on: April 16, 2021, 12:24:54 pm »

Thanks for reporting the issues on analyzing new PDB entries on Web 3DNA 2.0.

Is there a lag time between when a PDB deposit is made vs. when it's able to be accessed in the web server?

As mentioned in the Li et al 2019 paper (https://doi.org/10.1093/nar/gkz394)

To facilitate the analysis of nucleic-acid-containing structures from the PDB, a very common user demand, we constructed a database of those entries for w3DNA 2.0. The current database is populated by all PDB entries (with metadata) from the 6 March 2019 release that contain the 3D coordinates, in traditional PDB format, of at least one nucleotide. Gigantic structures, such as the ribosome, that are available only in PDBx/mmCIF format are thus excluded from the database.

No new PDB entries after 2019-03-06 are auto-processed on the current Web 3DNA 2.0 web server. See also the thread "w3dna server update schedule?"

The project is currently out of funding support, and the service is provided AS IS. Things may change/improve in the future, though.

Best regards,

Xiang-Jun

171

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

« on: April 13, 2021, 03:43:40 pm »

Hi,

The source code of 3DNA v2.4 is available for academic users from this Forum. You should see the "Downloads" page after verification of your registration email. DSSR is licensed by CTV, and is distributed in binary executable forms only.

Xiang-Jun

172

RNA structures (DSSR) / Re: force DSSR to treat the loop region as base-pairs

« on: April 11, 2021, 05:50:17 pm »

Hi,

Yes, DSSR Pro can do it. DSSR Pro also includes many advanced features, enhanced usability, and support that are not available in the basic version.

Best regards,

Xiang-Jun

173

General discussions (Q&As) / Re: Support for batch processing?

« on: March 06, 2021, 11:55:44 am »

Hi,

Is there a way to use this command on a batch of sequences to generate separate .pdb files for each sequence without manually entering each sequence into the command line?

You may have already found a solution to the above question. As a follow-up, the fiber module in DSSR Pro has more advanced features and much better usability than 3DNA, including such batch processing.

Xiang-Jun

174

RNA structures (DSSR) / Re: Query in 3DNA-DSSR output vs W3DNA output

« on: February 28, 2021, 10:22:26 am »

Hi,

Thanks for using DSSR and 3DNA, and for posting your question on the 3DNA Forum.

For a duplex with N base pairs, there are N-1 base-pair steps. In the 3DNA suite of programs, the analyze program produces a file with content like below (using your attached example):

   8 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G-C     -0.270    -0.132    -0.197    -0.052     1.100     4.414     0.000     0.000     0.000     0.000     0.000     0.000
A-T     -0.499    -0.435     0.176     1.262   -10.089   -12.655    -1.694    -0.607     3.330    -2.903    -4.465    34.601
G-C     -0.115     0.069     0.407     5.730    -4.240    10.116     0.638    -0.387     3.180    -0.622     0.059    39.925
G-C     -0.876    -0.275     0.220     8.648    -3.894    -3.932    -0.713     0.224     3.224    -0.525     4.756    27.462
C-G      0.513    -0.078     0.087    12.122   -13.041    -1.249     0.731    -0.167     3.314     1.351     2.611    38.586
T-A     -0.066    -0.076     0.266   -17.997    13.206    -0.182     2.088     2.132     7.857   -17.640     5.211    44.686
T-T      1.892    -1.893     0.406     0.252     7.615     6.070     1.058     0.614     3.339    -4.474    11.137    38.739
A-A     -4.400     1.650     0.278   -10.936     4.849  -115.147    -8.924    -0.354     6.529   -34.317    10.409    20.463

The 3DNA rebuild program can then read this parameter file and build a model accordingly. Here the six parameters (highlighted in red) along with the first base pair are just space fillers. ANY numeric values will serve the purpose.

Now in DSSR, I have changed the format as below:

# 7 (no. of base pairs)
#bp      Shear     Stretch    Stagger    Buckle   Propeller   Opening      Shift      Slide      Rise       Tilt       Roll       Twist
G-C    -0.2701    -0.1317    -0.1971    -0.0521     1.0996     4.4143    -1.6945    -0.6073     3.3302    -2.9026    -4.4649    34.6011
A-T    -0.4989    -0.4352     0.1758     1.2619   -10.0888   -12.6549     0.6376    -0.3870     3.1803    -0.6220     0.0588    39.9253
G-C    -0.1149     0.0686     0.4070     5.7305    -4.2403    10.1156    -0.7126     0.2239     3.2238    -0.5251     4.7555    27.4624
G-C    -0.8762    -0.2749     0.2201     8.6484    -3.8937    -3.9324     0.7312    -0.1669     3.3143     1.3511     2.6115    38.5859
C-G     0.5131    -0.0780     0.0868    12.1222   -13.0413    -1.2495     2.0883     2.1322     7.8572   -17.6400     5.2115    44.6864
T-A    -0.0657    -0.0764     0.2658   -17.9967    13.2060    -0.1819     1.0584     0.6138     3.3386    -4.4736    11.1373    38.7389
T-T     1.8918    -1.8929     0.4065     0.2517     7.6152     6.0696     999999     999999     999999     999999     999999     999999

The number 999999 in DSSR makes the space-filling purpose of the six extra step parameters more obvious than 0.000 in 3DNA. They are put into the line with the final base pair as I feel this arrangement more natural. Most importantly, the DSSR output is intended to be fed into a modeling module of DSSR Pro, not to be used with the original 3DNA rebuild program.

The --analyze option has been removed from DSSR as of version 2.0 to avoid the confusion you experienced. Thus DSSR basic does not have this feature any more, whilst DSSR Pro has a new, much enhanced module in its place. DSSR Pro has completely superseded 3DNA, with a streamlined user interface and many advanced features (especially in modeling).

Best regards,

Xiang-Jun

175

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

« on: February 24, 2021, 11:57:13 am »

Hi Brinda,

Thanks! Please let me know once you get the DSSR Pro Academic license. We will follow up from there.

I am positive that DSSR Pro users will feel that the software and quality service is worth the price.


Best regards,

Xiang-Jun