[phenixbb] Improvement of low resolution MR phases

Jrh Gmail jrhelliwell at gmail.com
Tue Jun 29 05:38:58 PDT 2021


Dear Tommi
Please see my comments interspersed below
Best wishes
John


Emeritus Professor of Chemistry John R Helliwell DSc_Physics 


> On 29 Jun 2021, at 13:23, Kajander, Tommi A <tommi.kajander at helsinki.fi> wrote:
> 
> 
> Dear John, 
> 
> Thanks for your suggestion - however I am not sure what this would mean? If look at the typical Wilson plot (which we of couse dont really have ... to 2 Å or 2.5Å) why would you expect an increase in intensity at this resolution?

The choice of 2 1/2 Ang resolution is just where, approximately, I imagine the molecular transform rises again. 
The reciprocal lattice selects the intensity of the molecular transform ie at its lattice points.


> 
> Probably beyond my theoretical knowledge but I don't recall a case where the data would come back up in terms of I(sig) to above noise really? 
Your sort of case is to my knowledge rare, let alone shared on a bulletin board, and secondly the rise of the molecular transform as I suggest above is maybe insufficient to get above background. 

> (also in practical terms I think we might not have had the detector close enough since the data was limited to quite low resolution…)
Chance of a remeasure?

> 
> Best wishes,
> Tommi
> 
>>> On 29 Jun 2021, at 11:13, John R Helliwell <jrhelliwell at gmail.com> wrote:
>>> 
>>> Dear Tommi,
>>> I have thought before about this kind of case, of 5 to 6 Angstrom resolution diffraction, namely that the molecular transform must increase again at higher resolution, say 2 1/2 Angstrom, at which therefore the measurable intensity would increase enough to maybe be above background. 
>>> To check this go back to your diffraction images and integrate to, say, 2Angstrom. Does the <I/sigI> show the increase at around 2 1/2 Angstrom resolution?
>>> Obviously if you do have those higher resolution data measurable then matters improve all round.
>>> Greetings,
>>> John 
>>> 
>>> Emeritus Professor John R Helliwell DSc
>>> 
>>> 
>>> 
>>> 
>>> On 28 Jun 2021, at 12:56, Kajander, Tommi A <tommi.kajander at helsinki.fi> wrote:
>>> 
>>>  Hello all,
>>> 
>>> I was wondering what would be current best protocols for trying to improve maps/phases for low resolution 
>>> MR / refinement solutions (5-6 Å resolution). 
>>> 
>>> High solvent content of course, dimeric 2:2 protein complex so some NCS averaging and density modification
>>> I assume might help (related structures known, currently maps very blobby, clear solution but I think should be able to do better...).
>>> 
>>> Also, refinement suggestions welcome.
>>> 
>>> Best route in phenix? So far worked initially with ccp4. Other suggestions also welcome.
>>> 
>>> Thanks!
>>> Tommi
>>> 
>>> 
>>> Tommi Kajander, Ph.D. 
>>> Institute of Biotechnology
>>> University of Helsinki
>>> Viikinkaari 1 (P.O. Box 65)
>>> 00014 Helsinki, Finland
>>> p. +358-50-4480991
>>> http://www.helsinki.fi/kajanderlab
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
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> 
> Tommi Kajander, Ph.D.
> Structural Biology and Biophysics
> Institute of Biotechnology
> University of Helsinki
> Viikinkaari 1 (P.O. Box 65)
> 00014 Helsinki, Finland
> p. +358-2-941-58904 / +358-050-4480991
> tommi.kajander at helsinki.fi
> http://www.helsinki.fi/kajanderlab
> 
> 
> 
> 
> 
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