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Questions and answers => DNA/RNA-protein interactions (SNAP) => Topic started by: shuxiang on July 26, 2019, 03:18:55 pm

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Title: What are the Tdst and Rdst meaning?
Post by: shuxiang on July 26, 2019, 03:18:55 pm

Hi Xiang-Jun,
I used snap to calculate the interactions between RNA and proteins and a partial output likes this:
       id   nt-aa   nt           aa              Tdst    Rdst     Tx      Ty      Tz      Rx      Ry      Rz
   1  2ZJP  A-lys  X.A5         G.LYS162         7.87   62.37   -7.80    0.04   -1.04   53.25   26.79   19.25

Wilma and I are wondering that the meanings of Tdst and Rdst (We guess they are transnational distance and Rotational distance). But why these distances can be negative values?

Thank you. :)

Best,
Shuxiang

Title: Re: What are the Tdst and Rdst meaning?
Post by: xiangjun on July 26, 2019, 03:29:52 pm

Hi Shuxiang,

Tdst and Rdst mean translational and rotational distances, respectively. The negative values reflect the relative position (e.g., the C-alpha atom above or below a base plane).

Xiang-Jun
 

Title: Re: What are the Tdst and Rdst meaning?
Post by: shuxiang on July 26, 2019, 03:32:24 pm

Great. Thank you.

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University