Recent Posts

21

RNA structures (DSSR) / Re: dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« Last post by xiangjun on October 21, 2021, 09:47:35 pm »

DSSR is behaving as designed. Please see the section "Identification of nucleotides" of  the 2015 DSSR paper:

A nucleotide is identified if a residue contains at least three base ring atoms and the root-mean-square deviation (rmsd) of the fit falls below a user-definable cutoff. Since base rings are rigid, the rmsd is normally <0.1 Å. To account for experimental error and special non-planar cases, such as 5,6-dihydrouridine (H2U) in yeast tRNA^Phe (Figure 2), the default rmsd cutoff is set to 0.28 Å.

The default DSSR cutoff values are based on extensive tests in real-world applications. Any unidentified nucleotide is almost always due to heavy distortions in its base geometry that is 'beyond recognition'. For example, G248 in your attached 6nd42.pdb file has the PyMOL rendered image as attached. Note the N1-C2 distance is 2.2 Å, far larger than ~1.5 Å (the normal covalent C-N bond length).

DSSR Pro has provisions to handle extreme cases like yours.

22

RNA structures (DSSR) / dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« Last post by zcx on October 21, 2021, 07:52:52 pm »

I am using dssr version v1.9.10-2020apr23 to analyze PDB 6nd4 chain 2. There are 146 standard nucleotides in this chain. However, when I run

x3dna-dssr -i=6nd42.pdb  -o=output.dssr

It reports
    total number of nucleotides: 144

This also causes the dssr-2ndstrs.dbn files to have 144 rather than 146 positions. It seems dssr disregard residue G248 for unknown reason.

23

RNA structures (DSSR) / Re: DSSR output

« Last post by xiangjun on October 07, 2021, 09:47:56 am »

Which version of DSSR are you using?

24

RNA structures (DSSR) / DSSR output

« Last post by kirkpacc on October 07, 2021, 06:54:00 am »

I am running DSSR from within a python program using os.system().  It works well, but I would like to suppress all of the screen output.  I can redirect the screen output, but would prefer that it did not happen at all.  Is there an option to set to do this?

25

w3DNA -- web interface to 3DNA / Re: why w3DNA fails to calculate some non-canonical base pairs in structure

« Last post by xiangjun on September 16, 2021, 11:30:57 am »

Hi Ying,

Given the information you provided, I can only conclude that there must be some oddity in your structure at the places where 3DNA is unable to detect the base pairs. I cannot provide any further advice before seeing the structure (or the relevant section of it).

Xiang-Jun

26

w3DNA -- web interface to 3DNA / Re: why w3DNA fails to calculate some non-canonical base pairs in structure

« Last post by Ying on September 16, 2021, 10:21:36 am »

Dear Xiang-Jun,

Attached please find the part of analysis done via w3DNA for my PDB, and I found that the analysis just escape 4 adenosines for all types of calculation. The sequence (5'---3') is GGGC(CAG)5GUCC. Thank you very much for your help.

Best wishes,

Ying

27

w3DNA -- web interface to 3DNA / Re: why w3DNA fails to calculate some non-canonical base pairs in structure

« Last post by xiangjun on September 15, 2021, 01:52:03 pm »

Please provide a concrete example.

28

w3DNA -- web interface to 3DNA / why w3DNA fails to calculate some non-canonical base pairs in structure

« Last post by Ying on September 15, 2021, 01:49:25 pm »

Dear Xiang-Jun,

I used the 3DNA web sever before, but there are several base pairs missing during the calculation, which may result in the incorrect calculation for the width of the major and minor groove of our RNA structure. I searched the forum and found that it may be due to the default setting for the website. Could you give me some suggestions on this problem?  Thank you very much for your help.

Best wishes,

Ying

29

RNA structures (DSSR) / Re: How to get DSSR up and running?

« Last post by Ying on September 15, 2021, 01:41:25 pm »

In addition, I tried the DSSR web server, it failed because there was an error: Data too long for column 'jobid' at row 1.

Dear Xiang-Jun,

Thanks for your reply.
For the one I mentioned that DSSR web failed to analyze the structure, it is not the RNA structure 4J50, it is a new structure we solved and I have not published it.

The reason I took 4J50 as an example, is to confirm with you that whether DSSR basic will provide the groove width analysis.

Thank you very much again.

Best wishes,

Ying

30

RNA structures (DSSR) / Re: How to get DSSR up and running?

« Last post by xiangjun on September 15, 2021, 11:56:26 am »

Hi Ying,

I am sorry that I forgot to update you on the progress.
Yes. I have downloaded the DSSR basic.

It is beneficial to update each topic you began so that other readers have a complete knowledge of what has occurred.

After I downloaded the DSSR software, I decompressed it and there are two files (DSSR manual and x3dna-dssr.exec) without further installation. I tried both computers, attached please find two images after I opened the .exec file. It seems that the software did not work. Is there anything wrong?

DSSR was designed with simplicity in mind. There are just two files distributed: a self-contained binary executable [x3dna-dssr (macOS and Linux) or x3dna-dssr.exe for Windows] as well as the associated PDF user manual. Because DSSR is a command-line software, it must be executed from a terminal window.

From the screenshot you attached, you are on macOS and DSSR is running as expected. Presumably, you've double-click x3dna-dssr to run it, as shown below:

x3dna-dssr ; exit;

So DSSR simply prints some help message and then exit. You must have a basic understanding of how to execute command line programs on macOS to run DSSR.

missing required option: must specify -i=PDBFile/mmCIF

type: 'x3dna-dssr -h (or --help)' for further help
      'x3dna-dssr --citation' for preferred citation(s)

Time used: 00:00:00:00

[Process completed]

Next, let me explain why I want to download the software DSSR. I used the 3DNA web sever before, but there are several base pairs missing, which may result in the incorrect calculation for the width of the major and minor groove of our RNA structure. I searched the forum and found that it may be due to the default setting for the website.  So I want to download the software and reset the parameters to see whether it can recognize the base pairs and measure the width again.

3DNA v2.4 is open source and is available to academic users after registering on the 3DNA Forum. If you have any particular queries about 3DNA v2.x, please submit them in the "General discussions (Q&As)" or "w3DNA — web interface to 3DNA" section.

In addition, I tried the DSSR web server, it failed because there was an error: Data too long for column 'jobid' at row 1. I also tried to analyze one published RNA structure (4j50)

Web DSSR (http://wdssr.x3dna.org) is an unpublished work, therefore bugs are to be expected. However, it generally behaves as designed. I've just tried PDB entry 4j50 without a problem.

Please remember to include specifics so that others can REPRODUCE reported problems.

I found that there is no information about the groove width of the helix from DSSR web. So I wonder if the information will be provided by DSSR basic version?

DSSR Basic does not include some features of 3DNA v2.4; DSSR Pro does. As noted on the post "Clarification on DSSR licensing",  "DSSR Basic includes 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."


Users are encouraged to post any 3DNA/DSSR-related queries on the Forum. Please keep in mind to be detailed and to offer follow-up on each thread.

Best regards,

Xiang-Jun