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 :

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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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