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Hi Bernhard, <snip> > (c) looking at the next non-severe pinkish clashes, I notice that most involve > methyl groups, > > and if I eyeball them they are precisely staggered @60 deg around the H3C-X > torsion. But when 2 Leu > > for example are involved, I doubt that they face off at precisely that torsion > angle, because > > energetically this is a periodic potential. I think each methyl group torsion > would give a little > > bit, and voila, pink gone. > > In this case, I worry less about the pink, but how is this treated when riding > Hs are added in > > refinement, for the purpose of improved VdW restraints? Is this torsion > potential used (as > > in MD) or to we assume the 'hard' 60 deg stagger or nothing conformation? > Because if the > > torsion gives, also the C position might change slightly, ultimately resulting in > a more realistic > > model. Has anyone played with that? I cannot say anything about the inner workings in Refmac, but the CG-CD1 can CGCD2 are defined as rotatable bonds in the CCP4 dictionary: loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period LEU chi1 N CA CB CG 180.000 15.000 3 LEU chi2 CA CB CG CD2 180.000 15.000 3 LEU hh1 CB CG CD1 HD13 60.000 30.000 3 LEU hh2 CB CG CD2 HD23 60.000 30.000 3 So if you use torsion restraints (not default in Refmac AFAIK), you get a penalty, but the hydrogens can give way. In default settings the hydrogens will also give way enough. At least as far as I can tell. Cheers, Robbie > > > > Thx, BR > > > > *) which is best done at the very very end, because if you renumber residues > or sort waters, > > the extra occupancy keyword file needs to be changed as well; a process > whose tediousness > > is better not described. Indicative of errors in this file is a refmac infanticide > message > > child killed: SIGABRT > > > > **) or is there a more current version of the validation server already online? > > > > ***) Ceterum censeo coordinatae densitaeque providati eunt. > > > > ---------------------------------------------------------------------------- ------------ > > CVMO > > Vista, CA 92084 > > 001 (925) 209-7429 > > [log in to unmask] <mailto:[log in to unmask]> > > [log in to unmask] <mailto:[log in to unmask]> > > http://www.ruppweb.org/ <http://www.ruppweb.org/> > > ----------------------------------------------------------------------- > > > >