Messages

1

General discussions (Q&As) / Re: Comparing DSSR bp-pars,DSSR simple-bpParams,& find_pair|cehs local bp-parameters

« on: April 02, 2019, 09:07:04 am »

Hi Xiang-Jun,

Thank you for the clarification. Just to make sure I understood this properly, CEHS parameters should only be used to analyze conformational variations of WC structures. And since my structure has only parallel-stranded non-WC interactions, I should be using the base pair and step parameters outputted by x3dna-dssr --analyze?

Thanks,
Betty

2

General discussions (Q&As) / Re: Comparing DSSR bp-pars,DSSR simple-bpParams,& find_pair|cehs local bp-parameters

« on: April 01, 2019, 02:51:41 pm »

Hi Xiang-Jun,

I have attached the three output files, in the order of x3dna-dssr --analyze, x3dna-dssr --analyze-cehs, find_pair|cehs. Again, the local base-pair parameter values are quite different among the three files. The local base-pair step parameters are similar, but slightly different between --analyze-cehs and find_pair|cehs. And only the --analyze option outputs the local base-pair helical parameters. And all of the base pairs are noncanonical parallel-stranded interactions.

Thank you,
Betty

3

General discussions (Q&As) / Re: Comparing DSSR bp-pars,DSSR simple-bpParams,& find_pair|cehs local bp-parameters

« on: April 01, 2019, 02:09:28 pm »

Hi Xiang-Jun,

Thanks for your response. I ran my PDB file on x3dna-dssr --analyze, x3dna-dssr --analyze-cehs, and find_pair|cehs and ended up getting different local base-pair and local step parameter values for all three.  I also noticed that the x3dna-dssr --analyze option is the only one that gives local base-pair helical parameters. The other two do not output those values. Is there a way to get local base-pair helical parameters for --analyze-cehs and find_pair|cehs? I am not sure how to discern which output values would be most accurate for my PDB structure. All the interactions (that are observed in the helical portion) in my structure are parallel-stranded noncanonical base pairs. Knowing this, what command/option would you recommend using to obtain the most accurate parameters for my structure?

Thank you!
Betty

4

General discussions (Q&As) / Comparing DSSR bp-pars,DSSR simple-bpParams,& find_pair|cehs local bp-parameters

« on: March 29, 2019, 11:18:55 am »

Hi Xiang-Jun,
I ran DSSR and find_pair|cehs on the same pdb file and noticed that the base-pair parameter values for shear, stretch, stagger, buckle, propeller, and opening are all very different. Even in the same DSSR output file, the bp-pars (Line 6) have differences with the Simple-bpParams (Line 5). I have read through El Hassan and Callandine (1995), J. Mol. Biol, 251,648-664, but am still unclear about the mathematical basis for the parameters. Could you give a simple explanation as to why the values are different within the DSSR output file and between the DSSR and find_pair|cehs output files? How would you decide which values to use for structural analysis?
Thank you very much!
Betty

5

RNA structures (DSSR) / Quantifying base stacking interactions

« on: August 17, 2017, 03:07:53 pm »

Hi Xiang-Jun,

I am analyzing the base stacking interactions, which I generated using the --non-pair option, in my DNA model. If I were to quantify the amount of base stacking interactions by using the numbers in and out of parentheses, would the units just be Angstroms^2? And would you define these numbers as area of overlap of the bases?

Thank you!

Betty Chu