Hi Henry, You could try keeping selected atoms in the plane by manually editing restraints in the CIF. Set _chem_comp_plane_atom.dist_esd to something low. E.g.
loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd NAG-b-D plan1 N2 0.010 NAG-b-D plan1 C7 0.010 NAG-b-D plan1 O7 0.010 NAG-b-D plan1 C8 0.010 NAG-b-D plan2 C1 0.010 NAG-b-D plan2 C2 0.010 NAG-b-D plan2 C4 0.010 NAG-b-D plan2 C5 0.010 I would also check https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_chem_comp_plane_atom.dist_esd.html and try Grade2 https://grade.globalphasing.org/cgi-bin/grade2_server.cgi Best wishes, Tomas On Mon, Jun 12, 2023 at 11:06 AM Henry Padley <[email protected]> wrote: > > Hi all, > > > I'm trying to generate a CIF file of an iridium piano stool complex ligand > (Cp*Ir-Phenanthroline). > > Can Phenix eLBOW generate correctly restrained aromatic ring systems which > stay flat in refinement? > > The phenanthroline bonds in the output CIF are listed as "aromatic" in the > REEL text table but they are not recognised as such in refinement. I've tried > manually editing the CIF via this text table to produce the alternating > "double/single bond" structure but it still puckers slightly in refinement. > > My eLBOW input is a PDB file of the ligand (I have also tried SDF input). I > have tried Automatic and eLBOW AM1 QM settings. Might a different Geometry > optimisation software selectable within eLBOW generate the restrained > phenanthroline? > > Any advice greatly appreciated. > > > Henry Padley, MSci > School of Pharmacy > University of Nottingham > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please contact the sender and delete the email and > attachment. > > Any views or opinions expressed by the author of this email do not > necessarily reflect the views of the University of Nottingham. Email > communications with the University of Nottingham may be monitored > where permitted by law. > > > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
