Messages

101

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

102

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

103

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

104

General discussions (Q&As) / Re: Support for batch processing?

« on: March 06, 2021, 11:55:44 am »

Hi,

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

105

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):

   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

106

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

107

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
 

108

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

109

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:

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

110

w3DNA -- web interface to 3DNA / MOVED: composite DNA template length

« on: February 18, 2021, 11:09:00 am »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=952.0

111

General discussions (Q&As) / MOVED: Extending DNA in protein-DNA complex - issue with final steps

« on: February 18, 2021, 11:07:23 am »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=954.0

112

General discussions (Q&As) / MOVED: Circular DNA parameters

« on: February 18, 2021, 11:07:07 am »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=939.0

113

DNA/RNA-protein interactions (SNAP) / Re: How to download the SNAP code?

« on: February 17, 2021, 03:20:04 pm »

Hi,

Sorry to hear your trouble in downloading DSSR from the CTV website. Did you notice the "Express Licensing" tab at the top?

Over the past six months or so, the CTV has issued numerous DSSR licenses to users worldwide, mostly in academia. So obtaining DSSR is no longer a problem. At the beginning, some users got confused of registration on the 3DNA Forum to download 3DNA v2.4 and asking questions, and licensing of DSSR from the CTV.

Best regards,

Xiang-Jun

114

RNA structures (DSSR) / Re: Circular DNA parameters

« on: February 16, 2021, 08:56:51 pm »

As a follow-up, DSSR Pro now has modeling features that can produce circular DNAs and DNA super helices as shown below.

Best regards,

Xiang-Jun

115

RNA structures (DSSR) / Re: composite DNA template length

« on: February 11, 2021, 04:46:42 pm »

Hi,

I have created a brand-new program for template-based modeling of nucleic acid structures, including DNA-protein complexes. Now users can easily specify their own templates via the command-line. Using your 1kx5 as an example, one can easily build the attached model. See also two more complexes models.

This novel modeling program is distributed as a module of DSSR Pro.

Best regards,

Xiang-Jun

116

w3DNA -- web interface to 3DNA / Re: Binding site orientation in Composite

« on: February 11, 2021, 04:34:22 pm »

Hi,

I have created a brand-new program for template-based modeling of nucleic acid structures, including DNA-protein complexes. Now users can easily specify their own templates, as well as their orientations, via the command-line. This novel modeling program is distributed as a module of DSSR Pro.

Best regards,

Xiang-Jun

117

w3DNA -- web interface to 3DNA / Re: Composite

« on: February 11, 2021, 04:33:40 pm »

Hi,

I have created a brand-new program for template-based modeling of nucleic acid structures, including DNA-protein complexes. Now users can easily specify their own templates via the command-line. This novel modeling program is distributed as a module of DSSR Pro.

Best regards,

Xiang-Jun

118

RNA structures (DSSR) / Re: Extending DNA in protein-DNA complex - issue with final steps

« on: February 11, 2021, 04:28:33 pm »

Thanks for letting us know that you have now solved your problem on extending DNA at both ends in a DNA-protein complex. Template-based model building of DNA-protein complexes is a persistent issue, as demonstrated in this thread, the one you referred to, and the most recent questions on the Composite module of Web 3DNA 2.0. The traditional 3DNA-based approach 'works', but it is tedious and error prone. The process is technically challenging for non-expert 3DNA users. There are also certain inherent limitations in the approach, as you experienced.

I have created a brand-new program for template-based modeling of nucleic acid structures, including DNA-protein complexes. Using your example, extending 4wlw on 5'-end by fiber B-DNA duplex TTG and 3'-end by CTAACCT can be easily achieved. It literally takes only a couple of minutes. See the attached PDB coordinate file and a schematic image. This novel modeling program is distributed as a module of DSSR Pro.

Best regards,

Xiang-Jun

119

RNA structures (DSSR) / Re: Extending DNA in protein-DNA complex - issue with final steps

« on: February 03, 2021, 03:55:02 pm »

Hi,

Glad to know that you have figured out the issues. Instead of deleting your posts, could you please provide step-by-step procedure on how you solved the problem for the benefit of other users? The summary could also serve as a future reference for yourself.

Best regards,

Xiang-Jun

120

RNA structures (DSSR) / Re: composite DNA template length

« on: January 21, 2021, 09:46:41 pm »

Hi,

Thanks for your question on the Composite module in Web 3DNA 2.0. Composite is an advanced feature that mades use various 3DNA programs and ad hoc scripts. Other than the general idea, I honestly do not know how things work in details. Right now, I have no time to dig things up either. In the long run, I may consider to consolidate all these steps into a DSSR module to automate the process.

Shuxiang, the developer of Web 3DNA 2.0 but no longer involved in the project, may chime in with some insights.

Xiang-Jun

 

121

RNA structures (DSSR) / Re: x3dna-dssr -h no response

« on: January 15, 2021, 09:53:57 pm »

Hi,

• The 3DNA suite of programs (up to v2.4) has been superseded by DSSR. See the Overview PDF, especially Section 1.4 DSSR vs. 3DNA vs. SCHNAaP/SCHNArP.
• DSSR is licensed by Columbia University. It is available only through the website http://innovation.columbia.edu/technologies/CU20391
• 3DNA v2.4 (along with SCHNAaP/SCHNArP) is still available for downloaded from this Forum, but it is on longer developed/supported.

Hope this helps.

Xiang-Jun

122

RNA structures (DSSR) / Re: DSSR eta-base theta-base

« on: January 09, 2021, 07:19:44 pm »

Hi Cathy,

Happy 2021!

Following your request, I've updated DSSR so that the JSON output for pseudo-torsion angles eta_base and theta_base would be "null" instead of 0.0 when they cannot be calculated. I have also refined DSSR to account for chain breaks while calculating all pseudo torsions.

The updated DSSR (v2.2.1) will be available from the Columbia Technology Ventures (CTV) website, presumably by early next week. As you may know, DSSR is now licensed by Columbia University.

Best regards,

Xiang-Jun

123

General discussions (Q&As) / Re: How 3DNA calculate base overlapping?

« on: December 27, 2020, 02:28:29 pm »

Please read the 2003 3DNA paper and the 2015 DSSR paper.

Xiang-Jun

124

DNA/RNA-protein interactions (SNAP) / Re: How to download the SNAP code?

« on: December 27, 2020, 02:25:50 pm »

A quick note: SNAP has been integrated into DSSR, as of v2.2, and available for download from CTV.

Xiang-Jun

125

FAQs / Re: Where to download x3DNA

« on: December 08, 2020, 05:34:07 pm »

Hi Pawel,

You should now be able to see the Download section.

There is a lag from the time an account is activated to it being granted download access. The rules for registration/download have been tightening up to keep the Forum spam free, and to serve legitimate users only. I have updated the FAQ entry "How to make the best use of the Forum" to make the process more transparent.

Best regards,

Xiang-Jun