![]() Phenix.geometry_minimization 355d-3dna.pdb min.params You’ll need the most recently nightly build of Phenix (dev-1395 would work) and then run: Here’s a first go at refining just the backbone atoms of you input DNA model. Here is the mail reply from Jeff, using a 3DNA-generated DNA duplex ( 355d-3dna.pdb) as an example (see full details below): ![]() Particularly, Jeff Headd revised the geometry_minimization component of PHENIX to do the trick. At the meeting, I had the opportunities to talk to several members of the PHENIX team. The problem was finally solved after I attended the 43rd Mid-Atlantic Macromolecular Crystallography Meeting held at Duke University a few months ago. I tried but failed to find a satisfying third-party (command-line driven) tool that can perform restraint optimization of the sugar-phosphate backbone geometry while keeping base atoms fixed. Nevertheless, over the years, I have been concerned with the overlong O3′-P distance issue. The imprecise structure was intended as a starting point for other objectives (e.g., all-atom molecular dynamics simulations) that are out of the design scope of 3DNA. ![]() P(i+1) bond that connects consecutive nucleotides along a chain.The most noticeable effect is the long O3′(i) The backbone geometry is approximate because 3DNA uses a fixed sugar-phosphate conformation (in A- DNA, B- DNA or RNA) that is attached to the corresponding bases in the model building process. It was noted that The RMSD of reconstructed versus observed base positions is virtually zero and that for both base and backbone coordinates is <0.85 Å, even for the 146 bp nucleosomal DNA structure. In the 2003 3DNA- NAR paper, Table 3 of the section “Structures built with sugar–phosphate backbone” lists “root mean square deviation (in Å) between rebuilt 3DNA models and experimental DNA structures” for three representative DNA structures (in A-form, B-form, and a protein- DNA complex). 3DNA can build DNA/RNA structures with a precise base but approximate sugar-phosphate backbone geometry.
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