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Questions and answers => General discussions (Q&As) => Topic started by: chenlong on July 28, 2021, 08:12:15 am

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Title: Can the v2.4 x3DNA(mut_base)mutate more than one base at multiple sites of RNA
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!

Title: Re: Can the v2.4 x3DNA(mut_base)mutate more than one base at multiple sites of RNA
Post by: xiangjun on July 28, 2021, 08:56:59 am
DSSR Pro can do it and more.

Xiang-Jun
Title: Re: Can the v2.4 x3DNA(mut_base)mutate more than one base at multiple sites of RNA
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.
Title: Re: Can the v2.4 x3DNA(mut_base)mutate more than one base at multiple sites of RNA
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 (http://docs.x3dna.org/dssr-overview/).

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
Title: Re: Can the v2.4 x3DNA(mut_base)mutate more than one base at multiple sites of RNA
Post by: chenlong on July 29, 2021, 08:53:23 pm
Thank you for your reply.

Best wishes

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.