Messages

1

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

« 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

2

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

3

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

« 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

4

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

5

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

« 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

6

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

« 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

7

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