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