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Author Topic: How to get DSSR up and running?  (Read 1330 times)

Offline Ying

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How to get DSSR up and running?
« on: September 15, 2021, 12:55:39 am »
Dear Xiang-Jun,

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

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.

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), 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?

Thanks a lot for your help and I very appreciated it.

Best regards,

Ying

Offline xiangjun

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Re: How to get DSSR up and running?
« Reply #1 on: September 15, 2021, 11:56:26 am »
Hi Ying,

Quote
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.

Quote
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]



Quote
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.

Quote
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.

Quote
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
« Last Edit: September 15, 2021, 11:59:38 am by xiangjun »

Offline Ying

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Re: How to get DSSR up and running?
« Reply #2 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
« Last Edit: September 15, 2021, 01:43:36 pm by Ying »

 

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.