Topics

1

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

« 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

2

RNA structures (DSSR) / 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

3

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

« 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