Messages

101

General discussions (Q&As) / Re: Can the v2.4 x3DNA(mut_base)mutate more than one base at multiple sites of RNA

« on: July 28, 2021, 08:56:59 am »

DSSR Pro can do it and more.

Xiang-Jun

102

RNA structures (DSSR) / Re: how to repair a DNA model

« on: July 27, 2021, 11:48:48 am »

Please provide some background info and a concrete example to illustrate unambiguously what you want to achieve.

Thanks,

Xiang-Jun

103

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

« on: July 23, 2021, 06:17:33 pm »

Yes, I tried and finally manage to color differently at each nucleotide blocks.

Glad to know that you have managed to color nucleotide blocks as desired. This is an important first step for later on speed optimizations.

But it is quite slow since it make all individual block object for every nucleotide.

How many colors do you want to have? Grouping nucleotides with the same color should speed up the process. It is now a matter of PyMOL selection syntax to play with.

And also it print lots of warning messages during the run.
I can't locate the origin of this warning.
PyMOL>dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'

I cannot reproduce the warning messages. Let's not worry about them right now.

Best regards,

Xiang-Jun

104

Bug reports / Re: Uncaught exception error

« on: July 21, 2021, 09:50:10 pm »

Hi,

The DSSR version you used is v1.9.4-2019jul08. The latest DSSR version is v2.3.2-2021jun29, which works as expected for PDB entry 6jwe, as shown below:

Code: [Select]

x3dna-dssr --more --loop=with-stems --json -i=6jwe.pdb -o=6jwe.json

Processing file '6jwe.pdb'
    total number of nucleotides: 20
    total number of base pairs: 18
    total number of helices: 2
    total number of multiplets: 4
    total number of atom-base capping interactions: 2
    total number of splayed-apart dinucleotides: 2
    total number of non-loop single-stranded segments: 1
    total number of G-tetrads: 3
    total number of G4-helices: 1
    total number of G4-stems: 1
So please update your DSSR to the latest version (available exclusively from Columbia Technology Ventures).

Best regards,

Xiang-Jun

105

RNA structures (DSSR) / Re: Classical RNA loop motifs

« on: July 19, 2021, 08:49:19 am »

Hi Dr. Baulin,

As I understand correctly, for the moment there is no program (or database) that annotates (or stores) classical RNA loop motifs explicitly.
By the classical RNA loop motifs I mean sarcin/ricin loop, E-loop, tandem sheared G-A, GA/AAG internal loop, UAA/GAN internal loop, kink-turn, etc.

You may be right. Your list of 'classical RNA loop motifs' includes `etc.` and I am not sure/aware of the complete list.

As I know it:
1) only kink-turns are annotated by DSSR.

DSSR isn't intended to be a comprehensive tool for annotating 'classical RNA loop motifs.' DSSR, on the other hand, includes the fundamentals (such as base-pairing/stacking annotations and backbone torsions) that should make any downstream pipeline easier to annotate any well-defined RNA structural motifs.

DSSR can auto-detect kink-turns because K-turns have striking structural features and important functional roles, and I want to have a thorough understanding of the motif. Personally, I've found that only by implementing a topic/concept in detail source code can I truly comprehend it.

The Tamar Schlick made use of this DSSR features in their 2017 NAR paper "Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction." Please take a look at the following two threads (which also demonstrate the value of the 3DNA Forum) initiated by lead author of the paper:

• "Bending angle of internal loops"
• "1MZP"

2) for sarcin/ricin loop, E-loop, and tandem sheared G-A the best way of annotation is to use manually curated annotation from RNAMotifContrast and merge it with the RNA Motif Atlas clusters' identifiers.

RNAMotifContrast and RNA Motif Atlas clusters are certainly well-known resources on the topic. Another source of information that is worth checking is the Janusz Bujnicki lab website.

3) for GA/AAG internal loop and UAA/GAN internal loop annotation there are no existing ways at all.

DSSR has a dedicated section of ALL internal loops. Filtered by sequence constraints and geometric constraints, you might find what you're looking for.

If I'm wrong, could you please let me know if I missed anything?
If I'm right, are there any plans to add the mentioned motifs to DSSR functionality in the future?

In the future, I may add more motif annotations to DSSR Pro.

Best regards,

Xiang-Jun

106

RNA structures (DSSR) / Re: Removing some nucleotides and fixing/reducing the loop in my RNA structure

« on: July 19, 2021, 08:08:17 am »

In principle, I understand what you're trying to accomplish. However, I am unable to provide any concrete answers due to a lack of information.

107

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 12, 2021, 08:12:37 am »

Please pay close attention to my requests for clarification.

108

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 12, 2021, 06:56:59 am »

Code: [Select]

X.g1 - Z.C112;
X.G2 - Z.U111;
X.G41 - Z.A63;
X.G41 - Z.C82;
X.U42 - Z.A81;
X.U42 - Z.C82;
Are you sure this is the dot-bracket notation, with desired base-pairs you want???

109

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 11, 2021, 11:24:55 pm »

What the .dbn should be in this case (2YIE, between chains X and Z)?

110

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 11, 2021, 10:52:36 pm »

Please give specific examples of what you want to accomplish so that others can assist you. It's also a good way to get your thoughts straight.

111

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

« on: July 09, 2021, 03:49:05 pm »

OK. Let's forget about coloring DSSR blocks for the moment, focusing exclusively on PyMOL coloring of residues.

Could you color each nucleotide at each locations in PyMOL?

Now let G4 be G at position 4, the following will color its DSSR block yellow:

Code: Bash

1. select G4, resi 4
2. dssr_block G4, block_color='G:yellow'
3. # OR combined the above two steps as below:
4. # dssr_block resi 4, block_color='N:yellow'

Let Gs be selection of Gs at postions 5, 10, 11, do the following to color their blocks blue:

Code: Bash

1. select Gs, resi 5+10+11
2. dssr_block Gs, block_color='G:blue'
3. # OR combined as below:
4. # dssr_block resi 5+10+11, block_color='N:blue'

HTH,

Xiang-Jun

112

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 09, 2021, 10:18:24 am »

Only two chains? How about more than two chains? What do you mean by "the cross chain base_pair notation"?

113

RNA structures (DSSR) / Re: base-pair in dot-bracket notation in dbn file

« on: July 09, 2021, 09:10:54 am »

why number of base-pair in dot-bracket notation file (dssr.dbn) is not complete?

DSSR derives all base pairs (including noncanonical ones) in a given coordinate file. The .dbn output is for 2D structure with canonical pairs only.

Please read the 2015 NAR paper "DSSR: an integrated software tool for dissecting the spatial structure of RNA" thoroughly, perhaps several times, to gain a better understanding of the fundamentals. See also the post "Reproducing results published in the DSSR-NAR paper" and links therein.

Best regards,

Xiang-Jun

114

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 09, 2021, 09:10:12 am »

I get what you're saying, but I'm having trouble imagining how the requested new feature would be used. Please give specific examples to demonstrate what you're trying to accomplish.

Best regards,

Xiang-Jun

115

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

116

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

117

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

118

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

119

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

120

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

121

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

122

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

123

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

124

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

125

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