I am trying to build some DNA duplex models with different pitches by 3DNA. After changing the pitches from the original duplex model, I refined the duplex in PHENIX with geometry minimization. However, the basepairing get completely distorted. 

Is there a quick way to generate the cif file for basepairing in PHENIX or are there any other better ways to keep the basepairing restraint during the model refinement? 

Thank you very much for your kind help!

Sincerely,

Xiang    
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