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Hello!
I have a ssDNA/protein complex, its a little strange, the ssDNA coordinates are split into two (I see no loop).
I am having problems with analysis on the website (it is reporting only partial angles). Anyways I have tried to setup the standalone analysis input file and run it on the local computer but I am getting a little lost w/o a ssDNA input file example. Does anyone have ssDNA/protein examples?
thanks!
p.
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Thanks for posting your question on the forum and sending me the data. Your PDB file is an NMR ensemble consisting of 20 models. As you mentioned, the ssDNA is split into two parts, without a connecting loop.
You can run 'find_pair' with the -s option following by 'analyze', as shown below:
find_pair -s complex_ENSW_2.pdb ssDNA-protein.inp
analyze ssDNA-protein.inp
The list of nucleotides in your structure is in file 'ssDNA-protein.inp', with content:
complex_ENSW_2.pdb
complex_ENSW_2.outs
1 # single helix
14 # number of bases
1 1 # explicit bp numbering/hetero atoms
149 # ...1>B:..99_:[THY]T
150 # ...1>B:.100_:[THY]T
151 # ...1>B:.101_:[THY]T
152 # ...1>B:.102_:[THY]T
153 # ...1>B:.103_:[THY]T
154 # ...1>B:.104_:[THY]T
155 # ...1>B:.105_:[THY]T
156 # ...1>B:.299_:[THY]T
157 # ...1>B:.300_:[THY]T
158 # ...1>B:.301_:[THY]T
159 # ...1>B:.302_:[THY]T
160 # ...1>B:.303_:[THY]T
161 # ...1>B:.304_:[THY]T
162 # ...1>B:.305_:[THY]T
The parameters for the first model in your ensemble is in file "complex_ENSW_2.outs".
Please note the follows:
- Since your ssDNA is not in a helical conformation, the twist/rise/roll etc step parameters may not be useful; the backbone torsions have the normal meaning.
- Since you have an ensemble, you may want to analyze all of the 20 models to see variations along the chain. Currently, the Ruby script 'x3dna_ensemble analyze' applies only to duplexes. If needed, I will consider extending the script to ssDNA as well.
- Since you are studying a ssDNA-protein complex, the most interesting part maybe to know how ssDNA interacts with protein. Currently, 3DNA's analysis is nucleic-acid centered, i.e., without caring about the protein part. I am planning to extend 3DNA's functionality to the analysis of DNA-protein complexes from a more balanced point of view. As always, I welcome user feedback to make the forthcoming tool most relavant to real-world application.
HTH,
Xiang-Jun
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thanks! :)
do you have code for getting the ensemble angles with +/- standard dev?
p.
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No, as discussed previously in the forum.
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.
