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77
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
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
78
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
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
79
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.
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
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.
Quote
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
80
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
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
81
General discussions (Q&As) / MOVED: Stacking interactions in G-quadruplexes
« on: May 21, 2021, 11:48:32 am »82
General discussions (Q&As) / Re: The definition of glycoside conformation of guanine nucleotide in nucleic acid
« on: May 20, 2021, 10:26:25 am »Quote
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
83
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:
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
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
84
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
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
85
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
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
87
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
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
88
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
You've been granted access to the Download page.
Best regards,
Xiang-Jun
89
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
DSSR downloading from CTV should work again now. Please have a try and let us know how it goes.
Best regards,
Xiang-Jun
90
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:
I will post back when the issue is resolved.
Best regards,
Xiang-Jun
Thanks for reporting the DSSR downloading issue from CTV. Here is what I heard from them:
Quote
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
91
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.
As mentioned in the Li et al 2019 paper (https://doi.org/10.1093/nar/gkz394)
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
Quote
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)
Quote from: Datasets section of MATERIALS AND METHODS
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
92
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
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
93
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
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
94
General discussions (Q&As) / Re: Support for batch processing?
« on: March 06, 2021, 11:55:44 am »
Hi,
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
Quote
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
95
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):
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:
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
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
96
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
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
97
RNA structures (DSSR) / Re: nt_ids for residues i+1 and i-1
« on: February 19, 2021, 11:01:07 am »
Hi Brinda,
Thanks for your request for a new feature in DSSR. Without funding support, I am not able to devote time/effort to new features to DSSR Basic other than bug fixes. Further development and user support are thus being committed to DSSR Pro version only.
Best regards,
Xiang-Jun
Thanks for your request for a new feature in DSSR. Without funding support, I am not able to devote time/effort to new features to DSSR Basic other than bug fixes. Further development and user support are thus being committed to DSSR Pro version only.
Best regards,
Xiang-Jun
98
RNA structures (DSSR) / Re: 3DNA-DSSR
« on: February 19, 2021, 12:26:56 am »
In addition to my previous response, and just to clarify: Since August 2020 when DSSR became formally licensed, well over a hundred DSSR licenses have been issued via the CTV website. On average, that is approximately one license per week-day, to a total of 106 organizations world wide. As far as I know, all legitimate registrations have been promptly processed, thanks to the time/effort from the CTV support staff.
Xiang-Jun
Xiang-Jun
99
RNA structures (DSSR) / Re: 3DNA-DSSR
« on: February 18, 2021, 11:09:43 pm »
Hi,
DSSR is available exclusively via the CTV website. Note that "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."
The Download instructions post has the following explicit information:
Hopefully, the message is simple and clear enough.
Xiang-Jun
DSSR is available exclusively via the CTV website. Note that "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."
The Download instructions post has the following explicit information:
Quote
DSSR v2.2 has been released, with SNAP integrated into it. The stand-alone x3dna-snap program is gone and its functionality has been replaced by x3dna-dssr snap. Here is an overview of DSSR. DSSR has superseded 3DNA v2.4, with vastly expanded features and dramatically improved usability. Please visit the Columbia Technology Ventures (CTV) website to obtain a license and to download DSSR.
Hopefully, the message is simple and clear enough.
Xiang-Jun
100
w3DNA -- web interface to 3DNA / MOVED: composite DNA template length
« on: February 18, 2021, 11:09:00 am »Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.