Philippe You can use apply_peptide_plane=True to apply a plane to the atoms so it will be flatter regardless of the cis/trans configuration. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected] Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Mon, Sep 11, 2023 at 7:58 AM CUNIASSE Philippe wrote:

Dear all,

I am currently trying to refine a MDFF structure with the phenix RealSpaceRefine protocol of phenix.

I am wondering if it is possible to apply systematic restraints to peptide plane (in trans when they are trans and cis when they are cis in order to avoid twisted conformations of the peptide planes at the end of the refinement.

The only possibility I saw is to apply dihedral restraints defined one by one but when having thousands of residues, it seems not really convenient.

Thanks in advance for your help.

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: [email protected]

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

*[image: signature_863913621]*[image: signature_2053578832][image: signature_1816548304]

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