[phenixbb] (no subject)

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Thu Dec 3 04:53:35 PST 2009

Hi Ralf,

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
> conformations
> > 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.
> Ralf
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list