Recent Posts

51

RNA structures (DSSR) / Re: About the installation of dssr-basic windows version and linux version

« Last post by chenlong on July 29, 2021, 01:40:27 am »

I sincerely thank you for your reply. Through another attempt, I found a solution to the problem.

I wish you a happy work and life.

chen long

52

General discussions (Q&As) / Re: 3DNA manual

« Last post by chenlong on July 28, 2021, 09:52:34 pm »

Thanks for your reply,I will pay attention to it next time and sorry for my behavior.

53

General discussions (Q&As) / Re: 3DNA manual

« Last post by xiangjun on July 28, 2021, 09:16:09 am »

Check the $X3DNA/doc folder.

Remember to post specific questions in a new thread with a clear subject line.

Reading posts linked at "Netiquette" at the upper-left corner of the Forum should help.

Best regards,

Xiang-Jun

54

RNA structures (DSSR) / Re: About the installation of dssr-basic windows version and linux version

« Last post by xiangjun on July 28, 2021, 09:09:02 am »

Hi chen long,

1. After I got the academic license through Columbia University, I downloaded two versions of dssr-basic for linux and windows. But the windows version of the exe installation package can't open all the time. I have tried it on several computers with win7 and win10, but it doesn't work, so I would like to ask Dr. Lu why.

This is the first time I've heard of problems installing DSSR on Windows and Linux.

I do not understand what you mean by "But the windows version of the exe installation package can't open all the time." Does it work sometime? If so, when and under what condition? What do you mean by "it doesn't work"? Please provide screenshots to illustrate unambiguously the issues you experienced.

2. The files in the linux installation package are not in tar.gz format. I don't know how to install it. Could you please tell me. Or is there an installation method I haven't found? I did find it for a long time.

Then what format do you have from CTV download set? How long have you tried to find any other installation format?

It is fashionable these days to discuss the reproducibility of scientific publications. It's also crucial to ask questions in a consistent manner.

Best regards,

Xiang-Jun

55

General discussions (Q&As) / Re: Can the v2.4 x3DNA(mut_base)mutate more than one base at multiple sites of RNA

« Last post by xiangjun on July 28, 2021, 08:56:59 am »

DSSR Pro can do it and more.

Xiang-Jun

56

General discussions (Q&As) / Can the v2.4 x3DNA(mut_base)mutate more than one base at multiple sites of RNA

« Last post by chenlong on July 28, 2021, 08:12:15 am »

I am currently working on a project that uses 1o15.pdb
It is a structure where RNA and theophylline molecules are bound. I want to mutate the bases of different sites of RNA at the same time.
For example, ACGUACGUACGU mutates positions 2-6 and mutates more than one base to ANNNNNGUACGU, and creates a new PDB file with 4⁵ sequences. Can mutate_bases in X3DNA achieve this function?or it can use in dssr-basic. Thank you for your reply!

57

RNA structures (DSSR) / About the installation of dssr-basic windows version and linux version

« Last post by chenlong on July 28, 2021, 04:56:07 am »

Hello! I would like to share with you some recent issues regarding the use of DSSR. First of all, thank you for your great contributions to DSSR and X3DNA, which have helped many scholars and are free for academic institutions to use. My question is as follows:
1. After I got the academic license through Columbia University, I downloaded two versions of dssr-basic for linux and windows. But the windows version of the exe installation package can't open all the time. I have tried it on several computers with win7 and win10, but it doesn't work, so I would like to ask Dr. Lu why.
2. The files in the linux installation package are not in tar.gz format. I don't know how to install it. Could you please tell me. Or is there an installation method I haven't found? I did find it for a long time. So please let me know, thank you very much. 


Best wishes
chen long

58

General discussions (Q&As) / 3DNA manual

« Last post by chenlong on July 28, 2021, 01:33:34 am »

Hello, can I get a  the operation manual of x3DNA, 2.4  WINDOW version? I find but no result in this forum，sorry .

59

RNA structures (DSSR) / Re: how to repair a DNA model

« Last post by xiangjun on July 27, 2021, 11:48:48 am »

Please provide some background info and a concrete example to illustrate unambiguously what you want to achieve.

Thanks,

Xiang-Jun

60

RNA structures (DSSR) / how to repair a DNA model

« Last post by Garyren on July 27, 2021, 11:20:38 am »

I have a DNA model, however there are many broken chains in this model. I wonder if your DSSR can repair the broken DNA model?