Messages

151

General discussions (Q&As) / Re: How to setup 3DNA

« on: July 08, 2021, 07:43:24 am »

Hi Zw Han,

I have installed the 3DNA v2.4.4, but I can't use it. Could you please send me the manual of 3DNA. Thank you very much.

Please follow the instructions in $X3DNA/doc/README file.

Alternatively, you may find http://web.x3dna.org useful.

Best regards,

Xiang-Jun

152

FAQs / Re: Where to download x3DNA

« on: June 21, 2021, 08:32:16 am »

Hi Xingcheng,

I have registered a long time ago and used to be able to see the Download page. However, when I tried to download it just now, the page does not show up. Could I be granted the access again?

As noted in the FAQ "How to make the best use of the Forum" (http://forum.x3dna.org/faqs/how-to-make-the-best-use-of-the-forum/), private emails (gmail.com, yahoo.com, qq.com etc.) are no longer accepted on the 3DNA Forum. New registrations using private emails will be simply deleted. While previous such registrations (with posts), as in your case, are still kept, they do not have access to the download page any more.

Re-register on the 3DNA Forum using an identifiable (.edu) email, after activation, you will see the download page. Unactivated registrations will also been removed. I strive to keep this Forum spam-free and clean.

Hope this clarifies the issue.

Best regards,

Xiang-Jun

153

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

« on: June 01, 2021, 04:53:07 pm »

Hi Louis,

Thank you for confirming. The CTV website now has the DSSR Pro v2.3.1-2021jun01 available. If you have previously downloaded a version, please update to the latest version. If you have any questions, please let me know.

I greatly appreciate your support of the DSSR project by purchasing a Pro license. I sincerely hope you will find the quality of the software and my support to be well worth the money you have invested.

Best regards,

Xiang-Jun

154

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

« on: June 01, 2021, 03:28:20 pm »

Hi Louis,

Thank you for letting us know which browsers work and which don't when it comes to accessing the CTV websites. I've forwarded your findings to the DSSR-affiliated CTV support team. I'm guessing the problem isn't specific to the DSSR website on CTV, but rather a problem that affects a variety of websites.

My spotted case is 4w29 (a large ribosome), i am looking at chain BA, which starts with index_chain = 77, following chain AX's index_chain = 76.
I checked, the chains are not contiguous in space, nothing indicates they could be linked together. Other chains in the structure start at 1.

Now back to your initial question. I think it is a bug in DSSR that is only triggered in a rare case like 4w29: AX is an RNA chain, however, it has VAL77 at the end, as shown below:

ATOM   60690  C  C8    . A   X  24 76   ? 55.433   -163.384 92.500  1.00 140.84 ?  76   A   AX C8    1
ATOM   60691  N  N7    . A   X  24 76   ? 55.656   -163.215 91.217  1.00 141.03 ?  76   A   AX N7    1
ATOM   60692  C  C5    . A   X  24 76   ? 54.538   -162.520 90.779  1.00 141.71 ?  76   A   AX C5    1
ATOM   60693  C  C6    . A   X  24 76   ? 54.160   -162.033 89.512  1.00 142.30 ?  76   A   AX C6    1
ATOM   60694  N  N6    . A   X  24 76   ? 54.901   -162.183 88.412  1.00 143.14 ?  76   A   AX N6    1
ATOM   60695  N  N1    . A   X  24 76   ? 52.983   -161.377 89.410  1.00 142.62 ?  76   A   AX N1    1
ATOM   60696  C  C2    . A   X  24 76   ? 52.240   -161.228 90.513  1.00 142.49 ?  76   A   AX C2    1
ATOM   60697  N  N3    . A   X  24 76   ? 52.490   -161.642 91.754  1.00 142.54 ?  76   A   AX N3    1
ATOM   60698  C  C4    . A   X  24 76   ? 53.665   -162.290 91.829  1.00 141.84 ?  76   A   AX C4    1
ATOM   60699  N  N     . VAL X  24 77   ? 50.042   -163.172 98.420  1.00 50.64  ?  77   VAL AX N     1
ATOM   60700  C  CA    . VAL X  24 77   ? 51.296   -162.409 98.368  1.00 47.13  ?  77   VAL AX CA    1
ATOM   60701  C  C     . VAL X  24 77   ? 52.559   -163.283 98.400  1.00 44.56  ?  77   VAL AX C     1
ATOM   60702  O  O     . VAL X  24 77   ? 52.567   -164.326 99.054  1.00 40.69  ?  77   VAL AX O     1
ATOM   60703  C  CB    . VAL X  24 77   ? 51.361   -161.302 99.446  1.00 46.79  ?  77   VAL AX CB    1
ATOM   60704  C  CG1   . VAL X  24 77   ? 50.129   -160.404 99.438  1.00 47.04  ?  77   VAL AX CG1   1
ATOM   60705  C  CG2   . VAL X  24 77   ? 51.655   -161.873 100.828 1.00 46.46  ?  77   VAL AX CG2   1

With DSSR v2.3.1-2021jun01 (to be released), the index_chain starts at 1 instead of 77 for chain BA. Is that what you'd expect? Please confirm.

Best regards,

Xiang-Jun

155

Site announcements / Clarification on DSSR licensing

« on: May 31, 2021, 01:58:55 pm »

Once in a while I receive emails from prospective users, both commercial and academic, about DSSR licensing from the Columbia Technology Venture (CTV). Louis made the following explicit suggestion in a recent thread titled "Bug or feature (?) : residue numbering not understood":

I suggest you summarize the content of the [CTV] page in a forum post, to provide a reliable source of information about DSSR licensing, maybe?

There are two types of DSSR Pro licenses, as shown below:

• Commercial users may inquire about pricing and licensing terms by emailing techtransfer@columbia.edu (and CC to xiangjun@x3dna.org).
• Academic users can obtain DSSR Pro for a one-time fee of $1000, which includes a comprehensive user manual and one year of developer support as set forth in the license agreement. Please contact techtransfer@columbia.edu (and CC to xiangjun@x3dna.org). DSSR Pro has completely superseded 3DNA, and is being continuously improved.

Users of DSSR Pro, both commercial and academic, receive first-rate support directly from the developer. The open 3DNA Forum, private email, and virtual meetings are all options for contact, depending on what is most convenient for the users.

The free DSSR Basic academic license is no longer available as of November 11, 2021. Due to a lack of government funding, only DSSR Pro is offered for academic and commercial usage as outlined above. For further information, please visit the CTV DSSR website.

Xiang-Jun

156

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

« on: May 31, 2021, 12:04:14 pm »

Hi Louis,

Thank you for your input! The blank-page screenshot of the CTV DSSR website using the browsers/OSes you tested is surprising. It's possible that using HTTP rather than HTTPS is a problem. The 3DNA Forum, on the other hand, uses HTTP rather than HTTPS and apparently you can access it without difficulty.

I just tried using Firefox and discovered that the DSSR website on CTV was blocked by default, and I had to add columbia.edu to my trusted sites list to see the landing page. I've mostly used Safari and Chrome (on macOS) at work and haven't had any issues. As an example, see the screenshot from the CTV DSSR website. Because Chrome and Safari account for such a large percentage of browser usage, the CTV and many users may be unaware of the problem. Could you please try Chrome and Safari and report back your findings?

I'll inform the CTV team tomorrow (today is Memorial Day in the United States) about the access issue and the use of HTTP rather than HTTPs. Hopefully, things will turn around.

Best regards,

Xiang-Jun

157

RNA structures (DSSR) / Re: Incorrect topology assignment

« on: May 28, 2021, 09:52:45 pm »

Ok, I'll check these structures,

Please do. The more concrete examples, the better.

but it looks like our discussion goes beyond the canonical G-quadruplex structures (think in Webb da Silva's convention), hence the problems.

That is correct. Even 'canonical' G4 structures in the PDB have more complicated topologies than the Webb da Silva formalism allows. This is where DSSR can play a significant role: It can be used consistently on all G4s, and any "inconsistencies" are worth investigating further. Either DSSR needs to be improved (which I'd be delighted to do) or the structures themselves have some oddities (which is far more likely).

I look forward to the update if everything will be clearly explain in the publication. However, I hope that the "new convention" will be consistent with eg interpretations of CD spectra.

Do not expect to see a DSSR publication on G4 structures that have "everything clearly explained". For one thing, I have no idea on how a convention can "be consistent with eg interpretations of CD spectra". I simple do not have that expertise. Furthermore, the first DSSR paper dedicated to G4s may not be submitted/published anytime soon.

Unfortunately I am using the basic version of DSSR,  I have to think about buying the PRO version.

Hopefully, the DSSR Basic version and DSSR-G4DB have already been of some help to your project. If you decide to go for DSSR Pro, I may add an option that is tailored to your need.

There are many publications on structural analysis, annotations, and nomenclature of G4. If you find other free or more cost effective options, please let us know.

Best regards,

Xiang-Jun

158

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

159

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

160

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

161

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

162

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

163

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

164

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.

165

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.

166

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

167

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

168

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

169

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

170

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

171

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

172

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

173

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

174

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

175

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