Messages

76

RNA structures (DSSR) / Re: Where to download the DSSR basic version

« on: September 13, 2021, 10:16:10 am »

Hi Ying,

Thanks for your follow up. DSSR-related issues are always welcome.

I can see your registration for a DSSR Basic license, as given by the CTV, as of this writing. It is now Monday morning (New York time), which may explain the delay you are experiencing. DSSR licenses are often processed quickly by the CTV support staff. Please keep us informed on your progress. If you haven't heard back from CTV by the end of the day, I'll contact them about your situation.

Best regards,

Xiang-Jun

77

RNA structures (DSSR) / Re: Where to download the DSSR basic version

« on: September 10, 2021, 11:18:59 pm »

Hi Ying,

DSSR may only be downloaded from the Columbia Technology Venture (CTV) website. I've included a link to the CTV website in several places on this 3DNA Forum. I'm surprised that users like you are still having trouble locating where to get DSSR.

To clarify, I changed the header link "DSSR License" to "DSSR Download/Licensing". The DSSR download link is also included in my signature at the bottom of each of my posts. See also the post "Clarification on DSSR licensing".

Registration on the 3DNA Forum is required in order to obtain the classic 3DNA v2.4 (and SCHNAaP/SCHNArP), and ask 3DNA/DSSR-related questions.

Please let me know if there is anything else I can do to make this message crystal clear.

Best regards,

Xiang-Jun

78

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

« on: August 26, 2021, 12:04:19 pm »

As a followup, DSSR Pro now has the option to derive only pairs across chains.

79

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

« on: July 29, 2021, 09:17:15 am »

DSSR Basic does not have the base mutations feature at all. Also note that DSSR Basic is provided AS IS without any warranty of support.

That said, DSSR Basic does include features described in the three DSSR papers (2015 DSSR, 2017 DSSR-Jmol, and 2020 DSSR-PyMOL, all published in NAR) so that reported results can be reproduced. The DSSR Basic manual should function as expected. Anything to the contrary will be considered a bug and will be fixed as soon as possible.

DSSR Pro includes new advanced features, plus all functionality of 3DNA v2.4, as well as full support. Please watch the DSSR Overview Video.

Instead of DSSR/3DNA v2.4, you may want to try other software tools such as RNAView, FR3D, MC-Annotate, or Curves+ etc. Please let us know what you find.

Best regards,

Xiang-Jun

80

RNA structures (DSSR) / Re: About the installation of dssr-basic windows version and linux version

« on: July 29, 2021, 09:16:11 am »

Through another attempt, I found a solution to the problem.

Please elaborate on what you did that resulted in a solution to the problem.

Thanks,

Xiang-Jun

81

General discussions (Q&As) / Re: 3DNA manual

« on: July 28, 2021, 09:16:09 am »

Check the $X3DNA/doc folder.

Remember to post specific questions in a new thread with a clear subject line.

Reading posts linked at "Netiquette" at the upper-left corner of the Forum should help.

Best regards,

Xiang-Jun

82

RNA structures (DSSR) / Re: About the installation of dssr-basic windows version and linux version

« on: July 28, 2021, 09:09:02 am »

Hi chen long,

1. After I got the academic license through Columbia University, I downloaded two versions of dssr-basic for linux and windows. But the windows version of the exe installation package can't open all the time. I have tried it on several computers with win7 and win10, but it doesn't work, so I would like to ask Dr. Lu why.

This is the first time I've heard of problems installing DSSR on Windows and Linux.

I do not understand what you mean by "But the windows version of the exe installation package can't open all the time." Does it work sometime? If so, when and under what condition? What do you mean by "it doesn't work"? Please provide screenshots to illustrate unambiguously the issues you experienced.

2. The files in the linux installation package are not in tar.gz format. I don't know how to install it. Could you please tell me. Or is there an installation method I haven't found? I did find it for a long time.

Then what format do you have from CTV download set? How long have you tried to find any other installation format?

It is fashionable these days to discuss the reproducibility of scientific publications. It's also crucial to ask questions in a consistent manner.

Best regards,

Xiang-Jun

83

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

84

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

85

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

86

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

87

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

88

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.

89

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.

90

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???

91

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)?

92

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.

93

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

94

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"?

95

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

96

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

97

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

98

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

99

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

100

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