Dear all,

I am currently refining a protein-nucleic acid structure obtained by MDFF (NAMD) with a 2.9 Å cryo-EM map.

Dues to the poor density of the map at the end of the DNA duplex (likely due to breathing at the ends of the duplex), the structure of the DNA tends to be distorted.

I tried to set up a set of nucleic acid restraints (Base pairing and base stacking for the full sequence), however, despite the fact that the syntax was checked and no error message is present in the log file, it seems that the restraints are not taken into account as if the constant restraints were two weak. And indeed when examining the refined structure, the pairing and stacking restraints for the base pairs at the extremities of the DNA duplex are not fulfilled.

Have you a suggestion to solve this problem ?

Thanks in advance for your help.

Best regards.

Philippe.

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Philippe Cuniasse, PhD/HDR.

Institute for Integrative Biology of the Cell (I2BC)

UMR 9198 CNRS-CEA-Univ Paris Sud

Bat 144 CE-Saclay

91191 Gif-sur-Yvette Cedex, France

 

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