[phenixbb] How to exclude one part of a model to be taken into account during Real_Space_refinement ?

[CUNIASSE Philippe]

Dear all,
I am trying to do a phenix.real_space_refine in a CryoEM map at 4.2 Å with a model obtained by MDFF (NAMD, a protein DNA complex) because the resulting structure, despite a good CC and a good molecular geometry has a poor Ramachandran Map.
When doing the phenix.real_space_refine, the CC is slightly increased with respect to the starting structure, the Ramachandran is dramatically increased 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.
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.


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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 at cea.fr<mailto:philippe.cuniasse at cea.fr>
Web: http://biodev.cea.fr/rasmot3d/

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