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.inpThe 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
Topic: ssdna binding protein, again (Read 7848 times)