[phenixbb] Latest phenix from command line

Graeme Winter graeme.winter at googlemail.com
Mon Oct 5 08:45:55 PDT 2009


Hi Tom,

Yep, that hit the spot. After a little more fiddling got it working
just fine. Computer now nice and warm.

I'm running old and new side-by-side: will be interesting to see if
there are any differences.

Thanks again,

Graeme


2009/10/5 Thomas C. Terwilliger <terwilliger at lanl.gov>:
> Hi Graeme,
>
> You are right, for MAD/MIR you now want to use a parameters file rather
> than all command-line. I hope you'll like this better. I certainly do!
>
> For the problem you have I think the solution is simple:  one more "}" at
> the end of your mad.eff file.  If that doesn't do it, let me know!  I will
> see if I can make the error message more clear to say that the file cannot
> be read, not that it does not exist.
>
> All the best,
> Tom T
>
>>> Hi Folks,
>>>
>>> I'm one of those people who use the command-line for everything, and I
>>> just found my "phenix mad spell"
>>>
>>> phenix.autosol sites=8 atom_type=Se infl.data=TS03_12287_free.mtz   \
>>> infl.f_prime=-9.9 infl.f_double_prime=3.9 low.data=TS03_12287_free.mtz   \
>>> low.f_prime=-3.3 low.f_double_prime=0.5   \
>>> infl.labels='F_INFL SIGF_INFL DANO_INFL SIGDANO_INFL'   \
>>> low.labels='F_LREM SIGF_LREM DANO_LREM SIGDANO_LREM'
>>>
>>> no longer appears to work:
>>>
>>> Traceback (most recent call last):
>>>   File
>>> "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py",
>>> line 585, in <module>
>>>     run_autosol=run_autosol(args=sys.argv[1:])
>>>   File
>>> "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py",
>>> line 300, in __init__
>>>     self.Sorry(line)
>>>   File
>>> "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py",
>>> line 1238, in Sorry
>>>     raise AssertionError,e
>>> AssertionError: Sorry, unknown file or keyword:
>>> infl.data=TS03_12287_free.mtz
>>> Possibilities... (use 'phenix.autosol --help all' to get full help):
>>>   general.data_quality=TS03_12287_free.mtz
>>>   data=TS03_12287_free.mtz
>>>
>>> Looked at the doc and saw:
>>>
>>> MAD dataset
>>>
>>> The inputs for a MAD dataset need to specify f_prime and
>>> f_double_prime for each wavelength. You can use a parameters file
>>> "mad.eff" to input MAD data. You run it with "phenix.autosol mad.eff".
>>> Here is an example of a parameters file for a MAD dataset. You can set
>>> many additional parameters as well (see the list at the end of this
>>> document).
>>>
>>> autosol {
>>>   seq_file = seq.dat
>>>   sites = 2
>>>   atom_type = Se
>>>   wavelength {
>>>     data = peak.sca
>>>     lambda = .9798
>>>     f_prime = -8.0
>>>     f_double_prime = 4.5
>>>   }
>>>   wavelength {
>>>     data = inf.sca
>>>     lambda = .9792
>>>     f_prime = -9.0
>>>     f_double_prime = 1.5
>>>   }
>>>
>>> So I make mad.eff from information above, then
>>> -bash-3.2$ phenix.autosol mad.eff
>>> Traceback (most recent call last):
>>>   File
>>> "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py",
>>> line 585, in <module>
>>>     run_autosol=run_autosol(args=sys.argv[1:])
>>>   File
>>> "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py",
>>> line 155, in __init__
>>>     self.process_wizard_params(args)
>>>   File
>>> "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py",
>>> line 562, in process_wizard_params
>>>     self.Sorry("Unrecognized file or keyword: "+str(arg))
>>>   File
>>> "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py",
>>> line 1238, in Sorry
>>>     raise AssertionError,e
>>> AssertionError: Unrecognized file or keyword: mad.eff
>>>
>>> As listed in the instructions. Any clues, anyone?
>>>
>>> Many thanks in advance,
>>>
>>> Graeme
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>
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