[phenixbb] (no subject)
Schubert, Carsten [PRDUS]
CSCHUBER at its.jnj.com
Thu Dec 3 04:53:35 PST 2009
is this concept expandable to refining two or more ligands with
different resnames and atomnames on top of each other in the same
physical location using altlocs? I vaguely recall that phenix supports
this approach but have not tested it out myself yet.
Hypothetical case in point: 3 Ligands with resnames LG1, LG2 and LG3,
differing atomnames, all chain C and resi 1, altlocs from A to C. Is
something like this supported? What kind of requirements would I need in
order to do this?
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Ralf W. Grosse-Kunstleve
> Sent: Wednesday, December 02, 2009 3:55 PM
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] (no subject)
> Hi John,
> > I am looking for advice on how to best refine the structure of a
> complex that
> > has one component that can adopt two completely different
> conformations (a DNA
> > duplex). I can model both conformations and set occupancies to 0.5,
> and try to
> > constrain_group their occupancies, but in phenix.refine the two
> > are interpreted as major clashes.
> The trick to avoid the clashes is to set the "altloc" characters in
> column 17 of your PDB file. E.g. assign "A" to all atoms of the first
> conformer, and "B" to all atoms of the second.
> phenix.refine should correctly interpret your PDB file if you have
> a whole chain with altloc A followed by a whole chain with altloc B,
> assuming the chain id is identical and there are no TER cards between
> the conformers.
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