Recent Posts

91

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.

92

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

93

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

94

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

95

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

« Last post by Ying 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

96

RNA structures (DSSR) / Re: Where to download the DSSR basic version

« Last post by xiangjun on September 13, 2021, 10:16:10 am »

Hi Ying,

Thanks for your follow up. DSSR-related issues are always welcome.

I can see your registration for a DSSR Basic license, as given by the CTV, as of this writing. It is now Monday morning (New York time), which may explain the delay you are experiencing. DSSR licenses are often processed quickly by the CTV support staff. Please keep us informed on your progress. If you haven't heard back from CTV by the end of the day, I'll contact them about your situation.

Best regards,

Xiang-Jun

97

RNA structures (DSSR) / Re: Where to download the DSSR basic version

« Last post by Ying on September 13, 2021, 09:07:27 am »

Dear Xiang-Jun,

I am very sorry to interrupt you again. I have successfully submitted the application for the DSSR Basic licence on last Saturday. So far I have not received any information on the submission. I wonder is there anything else I can do to get the licence? Thank you very much for your attention and help.

Best regards,

Ying

98

RNA structures (DSSR) / Re: Where to download the DSSR basic version

« Last post by Ying on September 11, 2021, 04:25:05 am »

Dear Xiang-Jun,

I am sorry that I failed to catch up the information. Now it is clear enough for people like me to find the DSSR download information. I very appreciate it and thanks a lot.

Best regards,

Ying

99

RNA structures (DSSR) / Re: Where to download the DSSR basic version

« Last post by xiangjun on September 10, 2021, 11:18:59 pm »

Hi Ying,

DSSR may only be downloaded from the Columbia Technology Venture (CTV) website. I've included a link to the CTV website in several places on this 3DNA Forum. I'm surprised that users like you are still having trouble locating where to get DSSR.

To clarify, I changed the header link "DSSR License" to "DSSR Download/Licensing". The DSSR download link is also included in my signature at the bottom of each of my posts. See also the post "Clarification on DSSR licensing".

Registration on the 3DNA Forum is required in order to obtain the classic 3DNA v2.4 (and SCHNAaP/SCHNArP), and ask 3DNA/DSSR-related questions.

Please let me know if there is anything else I can do to make this message crystal clear.

Best regards,

Xiang-Jun

100

RNA structures (DSSR) / Where to download the DSSR basic version

« Last post by Ying on September 10, 2021, 10:53:11 pm »

Dear Sir,
I followed the instructions to register, got the confirmation link and logged in apparently properly, I did a lot research but still could not find the link to download the DSSR basic for academic study. Is the program still available?

Thanks
Ying