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.
>
>
>
>
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