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

[Oleg Sobolev]

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 at cea.fr
>
> Web: http://biodev.cea.fr/rasmot3d/
>
>
>
> *[image: signature_3454313285]*[image: signature_3433042689][image:
> signature_3416814468]
>
> -----------------------------------------------
>
>
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