Re: [phenixbb] Phenix crashes

Thanks for everyone. The link given by Nathaniel, works fine. ________________________________ From: Nathaniel Echols To: PHENIX user mailing list Sent: Thursday, September 10, 2009 11:52:17 AM Subject: Re: [phenixbb] Phenix crashes The parameters changed at some point this year, but the main documentation link is still for 1.4-3. We now have the nightly build documentation linked from the download page, e.g.: http://www.phenix-online.org/documentation/nightlies/1.4-147/automr.htm I suspect in this case it will be necessary to write a parameter file rather than use the command line. Fortunately, there is a very good example of this in the documentation. On Sep 10, 2009, at 9:44 AM, Randy Read wrote:

Did you cut and paste the command or retype it? If that's the exact command, I don't know what would be wrong with the bit "ensemble_1.coords=a1.pdb", but "ensemble_1_copies_to_find" should be "ensemble_1.copies_to_find" and "componenet" should be "component" and "_mass" should be ".mass". So I wonder if the parser got confused by the other syntax errors?

Regards,

Randy Read

On 10 Sep 2009, at 17:28, r n wrote:

...

Hi all

I am trying to use phenix.automr to search for two component.

Tried command line...

phenix.automr data=out.sca ensemble_1.coords=a1.pdb \ ensemble_1.RMS=0.65 ensemble_1_copies_to_find=5 componenet_1_mass=25000 \ component_1.component_copies=5 ensemble_2.coords=a2.pdb \ ensemble_2.RMS=0.60 ensemble_2.copies_to_find=5 componenet_2_mass=20000 \ component_2.component_copies=5

Following errors

phenix-installer-1.4-147/phenix-1.4-147/phenix/phenix/command_line/ automr.py", line 483, in <module> run_automr=run_automr(args=sys.argv[1:]) phenix-installer-1.4-147/phenix-1.4-147/phenix/phenix/autosol/ wizard_command_line.py", line 1237, in Sorry raise AssertionError,e AssertionError: Sorry, unknown file or keyword: ensemble_1.coords=a1.pdb

Not sure , What is wrong in my command?

Also try to use the Gui, but in automr gui only seen option for data file , not for model? May I am missing something?

Thanks

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------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www- structmed.cimr.cam.ac.uk

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------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected] _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb