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I was wondering if there is a way to 'idealize' the geometry of a DNA model - in terms of pushing it towards B-form and C2'-endo sugar puckering?The short answer is no. 3DNA does not 'idealize' an existing DNA model. However, there is a way around this 'deficiency'. See the FAQ entry "How do I build nucleic acid structures with sugar-phosphate backbone? (http://forum.x3dna.org/faqs/how-do-i-build-nucleic-acid-structures-with-sugar-phosphate-backbone/)" and my blog post titled "Restraint optimization of DNA backbone geometry using PHENIX (http://x3dna.org/highlights/restraint-optimization-of-dna-backbone-geometry-using-phenix)".
I have tried using 'find_pair *.pdb stdout | analyze stdin; x3dna_utils cp_std BDNA; rebuild -atomic bp_step.par *.pdb' and this provides a pdb file where the sugar pucker is corrected, and there are more sections which are B-form - however, the co-ordinates are shifted away from their current positions (and not all DNA sections are shifted in the same manner) and the chains are also renamed.The above procedure will generate a DNA model with exact base-pair geometry as in your original input PDB file, but only an approximate backbone: the sugars are all in C2'-endo as in the fiber model, and the O3'(i)--P(i+1) bond may well be out of the normal range. That's expected. You could use e.g. phenix (or other tools) to perform restraint optimization to get a more 'idealized' model.
I'm working on quite a large protein:DNA complex model to fit into an EM map and so would like to maintain the location and chain ID of the DNA co-ordinates and improve the geometry (to aid 'refinement' of this model against the EM map). What would be the best way to do this?
EXAMPLES
To set the Dickerson-Drew dodecamer CGCGAATTCGCG duplex structure
(355d.pdb) with its minor groove at the middle A6-T7 step facing
the viewer:
find_pair 355d.pdb stdout | analyze stdin
cp ref_frames.dat 355d_frames.dat
frame_mol -m -6,7 355d_frames.dat 355d.pdb 355d_new.pdb
and to rebuild a model with coordinates in the original frame:
rebuild -atomic bp_step.par 355d_f1.pdb
frame_mol -1 -r 355d_frames.dat 355d_f1.pdb 355d_raw.pdb
Check examples/calladine_drew/ subdirectory for more examplesFunded 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