Frank, Given that experimental electron density maps resulting from structure factors with a figure of merit of 0.5 are still interpretable, I don't think that "wiggling" the phases will be so bad. Fom of 0.5 corresponds to a phase error of 60 degrees, which is a pretty big shift.
Interesting thought you have regarding coordinate shifts disproportionately affecting higher resolution terms. Will have to think about that one a bit more!
Thanks,
Steve
> On Aug 18, 2017, at 3:18 AM, Frank von Delft <[log in to unmask]> wrote:
>
> 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 <[log in to unmask]> 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
>>>>
>>
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