No nucleotides identified from VMD selected ssDNA structure

[xiaoj12]

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

[xiangjun]

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.

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

[xiaoj12]

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

[xiangjun]

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