Hi Philippe,

but some part of the model ( in the case, the first three bases pairs a DNA duplex) are strongly distorted because of a lack of density in the corresponding region of the map.

This may be an indication that initial geometry of these first base pairs is poor and automatic secondary structure restraints cannot pick up these base pairs. Try to make sure you have Secondary structure restraints enabled and the base pairs in question are also restrained.

Best regards,

Oleg Sobolev.

For some reason, this does not append with the MDFF method.

I was wondering if there is a mean, in phenix.real_space_refine, to exclude a part of the model from being fitted in the map. Indeed, the distortion I observe in the DNA duplex is likely due to the fact that the real_space_refine tries to put the atoms at the extremity of the duplex in the closest density at the price of a strong distortion of the structure.

Thank in advance for your suggestions.

Best regards.

Philippe.

-----------------------------------------------

Philippe Cuniasse, PhD/HDR.

Institut de Biologie Integrative de la cellule.

UMR 9198 CNRS-CEA-Univ Paris Sud

Bat 144 CE-Saclay

91191 Gif-sur-Yvette Cedex

France

Tel: (33) 1 69 08 56 35

Fax: (33) 1 69 08 47 12

Email: philippe.cuniasse@cea.fr

Web: http://biodev.cea.fr/rasmot3d/

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