3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: xiaoj12 on November 24, 2015, 02:13:16 pm

Title: No nucleotides identified from VMD selected ssDNA structure
Post by: xiaoj12 on November 24, 2015, 02:13:16 pm: Dear Xiang-Jun,

Yep. Let's keep informed.

I experienced some issues when using DSSR today. The ssDNA I extracted from the a MD trajectory of the protein-DNA complex (using VMD selection cmd-select "nucleic") seems not be able to identified as a DNA/RNA chain by DSSR. I will attach the pdb I used (Frame1.pdb) and the relevant psf and pdb in expect in this post. Can you take a look at it when you had a chance?

Thanks!

JJ
Title: Re: No nucleotides identified from VMD selected ssDNA structure
Post by: xiangjun on November 24, 2015, 02:28:54 pm: Hi JJ,

Thanks for your follow up. The attached file, Frames1.pdb, is as shown below. It is not surprisingly that DSSR find any nucleotides in it.

(http://dssr.bio.columbia.edu/data/MD-ssDNA-Frames1.png)

On the other hand, 4DII_aptamer_autopsf.pdb is fine.

I am not familiar with VMD, or its selection command for that matter. But obviously, something is wrong in selecting and writing out full atoms for nucleic acids.

HTH,

Xiang-Jun
Title: Re: No nucleotides identified from VMD selected ssDNA structure
Post by: xiaoj12 on November 24, 2015, 02:49:45 pm: Hi Xiang-Jun,

Thank you for your fast reply. I saw similar thing you saw in VMD. I wonder how the visualization softwares (looks like pyMol you were using) and dssr determine the connections between atoms. I checked the atom orders in both pdbs I attached. They look the same.

JJ
Title: Re: No nucleotides identified from VMD selected ssDNA structure
Post by: xiangjun on November 24, 2015, 02:58:02 pm: Hi JJ,

I was using Jmol for visualization in this case. However, it does not matter: PyMOL or RasMol should give the same result. Basically, the atomic coordinates have been distorted. For verification purpose, you could select only a single nucleotide and write out its coordinates.

Alternatively, you'd be better off to seek for VMD support (I believe it has an active user community).

HTH,

Xiang-Jun