Dear Georg, Is it possible that your heavy-atom model includes S atoms as well as (or instead of) Ca atoms? For instance, SHELXD automatically makes a PDB file with atoms labelled as S regardless of what you’re looking for. If I provide the f’ and f” values for Ca atoms, I can only reproduce the Phaser error messages you report if the heavy-atom model includes at least one S atom. If they’re all Ca atoms, then there’s no problem. Presumably if the job passed on explicit scattering factors for S atoms to Phaser, it would also run. The Sasaki tables used to be fine for doing all relevant wavelength lookups, but now that longer wavelengths are experimentally accessible, we should look into other possibilities for table lookup of f’ and f” as a function of element type and wavelength. Best wishes, Randy ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

On 27 Aug 2018, at 09:04, Georg Mlynek wrote:

Dear Tom, thanks. Yes Phenix is the latest version 1.14-3225. I will put the data in the cloud.

Many thanks, br Georg.

On 2018-08-27 02:17, Tom Terwilliger wrote:

...

Hi Georg, I'm sorry for the trouble! I thought I had fixed the limitation of wavelength in autosol in March but I may have missed something! I think you are using a recent nightly build so your phenix should have whatever I did. If so, can you possibly send me the full log file and input files and I'll try it here and fix the wavelength problem? Thanks a lot! -Tom T

On Sun, Aug 26, 2018 at 2:42 PM, Georg Mlynek wrote: Dear Phaser Developers, we have collected data at diamond at 3A wavelength for Ca-MAD.

Running autosol supplying the peak and remote dataset I get a solution. However the resolution is too low for autobuild to be successful.

Therefore I continued with MR-SAD supplying the peak data=overall_best_refine_data.mtz This is my input mtz

However get this error message: Error message from Phaser: FATAL RUNTIME ERROR :Wavelength outside range of Sasaki tables. Use SCATTERING to specify f' and f" for atom(s) "S" Phaser phasing did not work

Scattering factors for Ca will be f'= -6.74 f''= 6.55 Using partial model pdb file as substructure: /home/g/r/aactn1_merge/phaser_31/aactn1_merge_phaser.1.pdb with RMS= 0.7 Data output to : AutoSol_run_32_/TEMP0/phaser_mtz FATAL RUNTIME ERROR :Wavelength outside range of Sasaki tables. Use SCATTERING to specify f' and f" for atom(s) "S" Phaser phasing did not work Analysis failed on solution evaluation

If I specify S as atom it continues without any problem however I get this warning, which I don't understand scientifically.

The same error I get (of course) when I would like to run PHASER-EP

I guess the errors are just resulting from the programs not adjusted to the longwavelength beamline.

Many thanks, best regards Georg.

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-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0033

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