Messages

151

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

« on: May 27, 2021, 06:55:32 pm »

In PyMOL, type: help dssr_block, you will see the following usage info:

Code: [Select]

dssr_block [ selection [, state [, block_file [, block_depth [, block_color [, name [, exe ]]]]]]]
From the DSSR-PyMOL paper on NAR (https://doi.org/10.1093/nar/gkaa426), download the Supplementary PDF. Section 3.2 in on "The --block-color option". In PyMOL, you use block_color, as documented from help dssr_block.

Combined, you would do the following in PyMOL:

Code: Text

1. # manual selection, named 'sele'; color any base red
2. dssr_block sele, block_color='N:red'

PyMOL has a flexible selection engine you may want to get familiar with.

Best regards,

Xiang-Jun

152

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

« on: May 27, 2021, 12:15:19 pm »

Hi Louis,

I will discuss with my team, but yes, we may go for it.

Thanks!

If the CTV team wants more information on the problem, do not hesitate to ask me (i tried with different browsers, but nothing succeeds).

Yes, please provide screenshots and post them here. I've contacted the CTV support team, and they will view this thread.

Best regards,

Xiang-Jun

153

RNA structures (DSSR) / Re: Incorrect topology assignment

« on: May 27, 2021, 11:31:15 am »

Let's agree to disagree on this point for the time being. The directionality in each G-tetrad is specified unambiguously using either "Major-->WC" or "WC-->Major". The first G-tetrad directs the assignment of the four strands of the G-quadruplex.

Please check the descriptors of the other PDB entries I listed, specifically 2GKU, 2LOD, and 4U5M if not more, including groove widths. Let me know if the descriptors are "correct" in your option. Overall, the strands assignment and the corresponding +/- loop directions follow certain convention. I've added a switch in DSSR Pro to allow for both, as user desire. I've been in direct communication with Dr. Webba da Silva for several years. I may change the current default settings later, when a paper on G4 (including G4DB) is published.

Best regards,

Xiang-Jun

154

RNA structures (DSSR) / Re: Incorrect topology assignment

« on: May 27, 2021, 10:31:12 am »

Hi,

Thank you very much for your feedback.

Technically, the assignment of clockwise (+) vs anti-clockwise (-) assignment is easy to change for these PDB entries with first G in syn conformation, thus the first G-tetard is ordered in Major-->WC direction. The current assignment in DSSR, by default, has considerations with regard to the calculation of rigid-body parameters (twist, rise, etc.). Following your feedback, it makes sense that the assignment of the descriptor is treated separately to follow the formalism of Mateus Webba da Silva.

How about the following for 2kqg:

List of 1 G4-stem
  Note: a G4-stem is defined as a G4-helix with backbone connectivity.
        Bulges are also allowed along each of the four strands.
  stem#1[#1] layers=3 INTRA-molecular loops=3 descriptor=3(-P-P-P) note=parallel(4+0) UUUU parallel
   1  glyco-bond=s--- sugar=.--- groove=w--n Major-->WC nts=4 GGGG A.DG2,A.DG18,A.DG14,A.DG6
   2  glyco-bond=---- sugar=---. groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
   3  glyco-bond=---- sugar=---3 groove=---- Major-->WC nts=4 GGGG A.DG4,A.DG20,A.DG16,A.DG8
    step#1  pm(>>,forward)  area=19.15 rise=3.41 twist=21.0
    step#2  pm(>>,forward)  area=12.05 rise=3.47 twist=28.2
    strand#1  U DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4
    strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20
    strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16
    strand#4  U DNA glyco-bond=--- sugar=-.3 nts=3 GGG A.DG6,A.DG7,A.DG8
    loop#1 type=propeller strands=[#1,#4] nts=1 C A.DC5
    loop#2 type=propeller strands=[#4,#3] nts=5 CACGA A.DC9,A.DA10,A.DC11,A.DG12,A.DA13
    loop#3 type=propeller strands=[#3,#2] nts=1 A A.DA17

While I am working on this topic, please also check (some of) the following PDB entries, and let me know your thoughts on the descriptors:

Code: [Select]

148d 186d 1bub 1c34 1c35 1c38 1hao 1hap 1hut 1i34 1qdf 1qdh 1rde 201d
230d 2e4i 2f8u 2gku 2hy9 2jpz 2jsk 2jsl 2jsm 2jsq 2kf7 2kf8 2kka 2km3
2kow 2kpr 2kqg 2kzd 2l88 2lod 2lyg 2m6v 2m6w 2m8z 2m91 2may 2mb3 2mbj
2mft 2mfu 2ms9 2mwz 2n2d 4dih 4dii 4lz1 4lz4 4ni7 4ni9 4u5m 5cmx 5ew1
5ew2 5j05 5j4p 5j4w 5j6u 5lqg 5lqh 5mjx 5mta 5mtg 5mvb 5o4d 5oph 5yey
5zev 6ac7 6ccw 6eo6 6eo7 6erl 6evv 6f4z 6fc9 6ftu 6gh0 6gn7 6gzn 6h1k
6ia4 6jkn 6jwd 6jwe 6kfj 6l8m 6l92 6r9k 6r9l 6rs3 6tc8 6tcg 6ycv 6yep
6z8v 6z8w 6z8x 6zx6 7atz 7cv3 7cv4 7ntu
Best regards,

Xiang-Jun

155

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

156

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

157

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.

158

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.

159

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

160

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

161

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

162

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

163

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

164

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

165

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

166

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

167

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

168

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

169

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

170

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

171

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

172

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

173

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

174

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

175

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