[phenixbb] autosol: FATAL RUNTIME ERROR :Wavelength outside range of Sasaki tables.

[Randy Read]

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: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk

> On 27 Aug 2018, at 09:04, Georg Mlynek <georg.mlynek at univie.ac.at> 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 <georg.mlynek at univie.ac.at> 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
>> <llckddahhjhjdpfg.png>
>> 
>> 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.
>> <cmblonbgeogodphd.png>
>> 
>> The same error I get (of course) when I would like to run PHASER-EP
>> 
>> <ankloeaopaghljbh.png>
>> 
>> 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: tterwilliger at newmexicoconsortium.org
>> Tel: 505-431-0033
>> 
> 
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