[phenixbb] How to model domain-wide disorder in Phenix.refine (turn off bump interactions) ?
pafonine at lbl.gov
Fri Feb 1 13:15:08 PST 2013
the only way to do it phenix.refine is to assign different altlocs to
overlapping atoms, say A to one domain and B to another one. Then they
will not "see" each other via non-bonded interactions.
Also, in this case phenix.refine will refine occupancies of these atoms
(which you can turn off if you wish). I guess by default it will group
occupancies such that A+B=1 per residue frame (may be not, I forgot how
I implemented it). That is for instance adjacent residues within A
conformer may have different occupancies; same for B.
Perhaps in your case you don't want this: having all occupancies to be
equal within each conformer would make more sense. You can do it by
using this syntax:
selection = chain A and resseq 1:100 and altloc A
selection = chain B and resseq 1:100 and altloc B
In this case all atoms in (chain A and resseq 1:100 and altloc A) will
have the same occupancy between 0 and 1, and same for (chain B and
resseq 1:100 and altloc B); and constraint occupacy_of(A) +
occupancy_of(B)=1 will be used.
Let me know if you need any help with this.
On 2/1/13 12:58 PM, Phil Jeffrey wrote:
> I've got a pernicious problem where the electron density for one
> domain appears to extensively interpenetrate another similar domain.
> I'm in the process of trying to work out things like: MR solution in
> the wrong space group courtesy of pseudo-centering. In the meanwhile I
> want to model it as interpenetrating domains, and need to turn off
> VdeW bumps at the domain (chain) level of structure. I can't just
> model it as a infinite list of alternate locations.
> I (think) I remember how to do this in CNS (constraints interaction),
> but is there a way to do this in phenix ? I could not track down a
> particularly promising section of either the manual or the .def/eff
> Phil Jeffrey
> phenixbb mailing list
> phenixbb at phenix-online.org
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