3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: Jian on November 27, 2014, 01:03:28 am

Title: A question about DSSR
Post by: Jian on November 27, 2014, 01:03:28 am: Dear Xiang-Jun,

I encountered a problem when I used DSSR for extracting the 2D structure of 3ZEX from its pdb file.

I issued the following command:
x3dna-dssr -i=3ZEX.pdb -o=3ZEX.dssr

Then I found that the '3ZEX.pdb' file contains totally 4200 nucleotides, while the '3ZEX.dssr' file concerns only 4177 nucleotides.

Thanks in advance!

Best regards
Jian
Title: Re: A question about DSSR
Post by: xiangjun on November 27, 2014, 12:14:00 pm: Hi Jian,

Thanks for using DSSR and posting your question on the 3DNA Forum.

Quote
Then I found that the '3ZEX.pdb' file contains totally 4200 nucleotides, while the '3ZEX.dssr' file concerns only 4177 nucleotides.
It'd have been helpful if you were specific as to which nts are not recognized by DSSR. Checking the PDB entry 3zex (http://www.rcsb.org/pdb/explore/explore.do?structureId=3zex), I found that this structure was solved by electron microscopy at a resolution of 5.57 Å. At such a lousy resolution, it is expected to see local distortions so that some nts are beyond 'recognition' (by default). One example is shown below, for A.G162: see how far off the six-membered ring is from the five-membered ring. Other 'missing' nts may well be due to similar reasons.

Note that chain breaks are represented by the symbol '&' in dot-bracket notation (dbn). You can also find DSSR-recognized nts in the "dssr-2ndstrs.ct" or "dssr-2ndstrs.bpseq" output files (run DSSR with the --more option).

HTH,

Xiang-Jun