[phenixbb] anomalous signal to ~5.1 - 4.5Å
Randy John Read
rjr27 at cam.ac.uk
Thu Dec 15 00:28:59 PST 2022
If you chose a peak wavelength for data collection on the basis of a fluorescence scan, then it would be better to use the measured f’ and f” values. If you’re not near the peak wavelength for your anomalous scatterer, then the table lookup that is done from the wavelength and atom type in the Phenix GUI is fine, and even if you’re near the peak wavelength it shouldn’t harm the phasing that much if you don’t have measured values.
> On 15 Dec 2022, at 07:18, Damon Wei <weizwann at gmail.com> wrote:
> 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
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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