[phenixbb] Latest phenix from command line

[Graeme Winter]

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