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1
Thanks for reporting the issues on analyzing new PDB entries on Web 3DNA 2.0.

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
2
A research assistant and I noticed an error upon searching for PDB IDs listed here using the "Analysis" tool on w3DNA 2.0: [6JVZ, 6JW4, 6JW3, 6JW5, 6JW0, 6JW2, 6JW1, 6JTQ, 6LEW]

Error Message: "ERROR: Empty or invalid ID, please type in a valid one."

These IDs are deposits dated either in 2019 or 2020. I did a search for 2021 deposits with DNA and did another set of 'Analysis' checks and, again, got the same error.

Is there a lag time between when a PDB deposit is made vs. when it's able to be accessed in the web server?
3
RNA structures (DSSR) / Re: Circular DNA parameters
« Last post by heesch on April 14, 2021, 06:23:14 am »
Dear Xiang-Jun,

That looks very pretty!!! Thank you very much for the follow-up!

Some while ago I managed to cook-up a "solution" using python by adjusting some of the elegant x3DNA parameters.
Sorry for not sharing my solution any sooner!


My approach assumed that every 10 basepairs one should adjust the roll angle to obtain a circle.
However, for sequences that have a length that is not a 10 fold I ran into issues, creating super helices...
So I randomly distributed the "remaining" basepairs among chunks of 10bp and adjusted the twist angle accordingly.

In the future I might work on building super coils!
Although, I have not had the time nor leads on how to do it ;D
So if anybody has some suggestions or ideas, I would be more than happy to hear them!


Here a snippet of python (v3) code to determine the new roll and twist parameters...
Code: [Select]
        import random
        import numpy as np



        n_bp = len(sequence)
   
 
        remainder = (n_bp % 10)
        if remainder != 0:

            raw_turns = n_bp / 10
            turns = int((n_bp-remainder) / 10)
            turn_angle = 360/turns
            bp_angle =  360/n_bp

            turn_indices = list(np.arange(0,n_bp,10))
            selection = sorted(random.sample(turn_indices[1:], remainder))

            count = 0
            new_turn_indices = []
            for index in turn_indices:
                if index in selection:
                    count +=1
                    new_turn_indices.append(index+count)
                else:
                    new_turn_indices.append(index+count)

            differences = [new_turn_indices[n]-new_turn_indices[n-1] for n in range(1,len(new_turn_indices))]
            turn_angles = [diff*bp_angle for diff in differences]

            count = 0
            roll_angles = []
            for i in range(0,n_bp):
                if i in new_turn_indices:
                    roll_angles.append(turn_angles[count])
                    count+=1
                else:
                    roll_angles.append(0)

            new_twist = 360/11
            twist = 360/10
            twists = []
            for diff in differences:
                if diff == 10:
                    twists.extend([twist]*diff)
                else:
                    twists.extend([new_twist]*diff)
   
4
RNA structures (DSSR) / Re: 3DNA/DSSR download issue
« Last post by naoto on April 13, 2021, 05:00:29 pm »
Thank you Xiang-Jun.

Somehow I could not see Download under the Welcome tab this morning, even after logging in with my account. But now I see the download page.

I appreciate you leave the code available.
Naoto
5
RNA structures (DSSR) / Re: 3DNA/DSSR download issue
« Last post by xiangjun 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
6
RNA structures (DSSR) / Re: 3DNA/DSSR download issue
« Last post by naoto on April 13, 2021, 02:09:21 pm »
Hello,

Is it correct that the source code of x3dna is no longer available even after agreeing to the CTV licence?

7
RNA structures (DSSR) / Re: force DSSR to treat the loop region as base-pairs
« Last post by xiangjun 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
8
RNA structures (DSSR) / force DSSR to treat the loop region as base-pairs
« Last post by amirtaghavi on April 11, 2021, 05:13:23 pm »
Hello Dr. Xiang-Jun,

I am using the DSSR to analyze a RNA structure (54 bps) with multiple repeats of (AUUCU) seq incorporating multiple 3x3 internal loops. As the structure is highly dynamic, many of the loops do not satisfy the conditions needed to be treated as a base-pair and naturally are skipped by the DSSR.
is there any way, other than manipulating the parameters which are used in DSSR to account for a base-pair, to force the DSSR to analyze all the 54 base-pairs irrespective of the defined criteria for base-pairs.

Thanks for your help.

Best,
Amir 
   
9
General discussions (Q&As) / Re: Support for batch processing?
« Last post by xiangjun on March 06, 2021, 11:55:44 am »
Hi,

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
10
RNA structures (DSSR) / Re: Query in 3DNA-DSSR output vs W3DNA output
« Last post by xiangjun 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
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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.