Recent Posts

41

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« Last post by xiangjun on August 26, 2021, 12:04:19 pm »

As a followup, DSSR Pro now has the option to derive only pairs across chains.

42

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 chenlong on July 29, 2021, 08:53:23 pm »

Thank you for your reply.

Best wishes

43

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 29, 2021, 09:17:15 am »

DSSR Basic does not have the base mutations feature at all. Also note that DSSR Basic is provided AS IS without any warranty of support.

That said, DSSR Basic does include 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. The DSSR Basic manual should function as expected. Anything to the contrary will be considered a bug and will be fixed as soon as possible.

DSSR Pro includes new advanced features, plus all functionality of 3DNA v2.4, as well as full support. Please watch the DSSR Overview Video.

Instead of DSSR/3DNA v2.4, you may want to try other software tools such as RNAView, FR3D, MC-Annotate, or Curves+ etc. Please let us know what you find.

Best regards,

Xiang-Jun

44

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

« Last post by xiangjun on July 29, 2021, 09:16:11 am »

Through another attempt, I found a solution to the problem.

Please elaborate on what you did that resulted in a solution to the problem.

Thanks,

Xiang-Jun

45

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 chenlong on July 29, 2021, 05:10:19 am »

Sorry to bother you again, but I would like to confirm if this feature is available in dssr-basic? Because I may not be able to afford the pro for now. I looked at the manual for basic and it doesn't seem to have this feature.

46

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

47

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.

48

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

49

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

50

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