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Author Topic: No nucleotides identified from VMD selected ssDNA structure  (Read 10502 times)

Offline xiaoj12

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No nucleotides identified from VMD selected ssDNA structure
« 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

Offline xiangjun

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Re: No nucleotides identified from VMD selected ssDNA structure
« Reply #1 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.


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
« Last Edit: November 24, 2015, 02:32:13 pm by xiangjun »

Offline xiaoj12

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Re: No nucleotides identified from VMD selected ssDNA structure
« Reply #2 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

Offline xiangjun

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Re: No nucleotides identified from VMD selected ssDNA structure
« Reply #3 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

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.