[phenixbb] anomalous signal to ~5.1 - 4.5Å

Damon Wei weizwann at gmail.com
Wed Dec 14 23:18:37 PST 2022

Dear Randy,

Thanks so much for your time and replies! Your messages are easy for me to
understand. I appreciate your thoughtfulness.

Yes, it is a protein structure. Your suggestion sounds great. A follow-up
question regarding the MR-SAD you mentioned: I think I have lost the file
containing the information of the anomalous coefficients (f' and f'', i.e.
Friedel pairs) somehow, but the wavelength λ is autofilled as 0.9707 when
I input the *.mtz* file. In this case, will the f' and f'' information be
converted or calculated automatically by the Phenix program?  I believe I
have read from somewhere that f' and f'' parameters are not required but
still highly recommended for SAD experiment. So I really wish to find a way
to provide the program with f' and f'' information if feasible.



On Wed, Dec 14, 2022 at 2:03 AM Randy John Read <rjr27 at cam.ac.uk> wrote:

> Dear Damon,
> Is this a protein structure? If it is and you haven’t tried molecular
> replacement with AlphaFold models, that’s what I would do first. With such
> limited anomalous signal, you’re unlikely to be able to solve the
> substructure and, even if you could, the phases would be unlikely to be
> good enough to build anything. On the other hand, if you had a molecular
> replacement solution, you could use MR-SAD to find the substructure and
> supplement the MR phase information. By the way, the Phenix GUI for
> Phaser-MR (full-featured version) helpfully offers a button to open a task
> to run MR-SAD, where you typically only have to enter the anomalous
> scatterer type and maybe wavelength or f” information.
> Best wishes,
> Randy Read
> > On 13 Dec 2022, at 22:12, Damon Wei <weizwann at gmail.com> wrote:
> >
> > You don't often get email from weizwann at gmail.com. Learn why this is
> important
> > Dear colleagues,
> >
> > During the past few days, I have been trying to perform Experimental
> Phasing (SAD) using AutoSol. I am really curious to know if any of you have
> ever had any successful experience for phasing with anomalous signal only
> to ~5.1 - 4.5Å. In this scenario, will you use the default value (2.38 Å)
> in the “high-resolution limit” option in AutoSol, or a higher value like ~
> 3-4 Å? How will you set the options including NCS copies, thoroughness, and
> resolution for running HySS?
> >
> > Any replies and help will be greatly appreciated!
> >
> > Best,
> > Damon
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> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research     Tel: +44 1223 336500
> The Keith Peters Building                               Fax: +44 1223
> 336827
> Hills Road                                                       E-mail:
> rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
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