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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
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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
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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
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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
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