Re: [phenixbb] Improvement of low resolution MR phases

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 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

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On 29 Jun 2021, at 11:13, John R Helliwell 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 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 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