[phenixbb] Latest phenix from command line

[Thomas C. Terwilliger]

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
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>>