On the same question, asked some time ago, Eleanor (or James?) pointed
out that the this perturbation changes the phases only of the higher
resolution reflections.
I believe the implied conclusion was that "resetting" a structure does
not have the same effect on all phases as randomising them all a bit
explicitly -- which is what people seem to think they want but would
produce garbage structures (or garbage maps), and ones that can't be
quickly fixed by a simple round of refinement.
That last bit is my interpretation; has anybody tested this?
phx
On 18/08/2017 07:51, Graeme Winter wrote:
Dear all,
Many thanks for all of your suggestions - it seems that I was looking with the
wrong search terms (perturb => shake) and there are indeed many tools out there
for performing this.
Problem solved :-)
Best wishes Graeme
On 17 Aug 2017, at 18:18, Victor Lamzin <vic...@embl-hamburg.de> wrote:
Dear Graeme,
You can also type the following on a command line, optional commands are given
in square parentheses.
Victor
$warpbin/arp_warp
mode shakemodel allatoms
files ccp4 xyzin FILENAME.pdb xyzout FILENAME.pdb
symmetry SPACEGROUP
shakemodel [ bexclude B1 ] [ breset B1 B2 ] [ randomise X ] [ shift X Y Z ]
end
On 17/08/2017 17:17, Graeme Winter wrote:
Dear All,
Is there a protocol out there to gently perturb atomic positions so that re-running
refinement can essentially put them back without bias from the original refinement? In
particular, if trying to perform the Karplus and Diederichs paired refinement protocol, I
do not want to run the lower resolution refinements with the "memory" of the
weak high resolution data present... and only have the refined structure to work from...
Am using refmac5, but any pdb randomizer would hit the spot
Many thanks Graeme
