<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Thanks for everyone.<br><br>The link given by Nathaniel, works fine.<br><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Nathaniel Echols <NEchols@lbl.gov><br><b><span style="font-weight: bold;">To:</span></b> PHENIX user mailing list <phenixbb@phenix-online.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thursday, September 10, 2009 11:52:17 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [phenixbb] Phenix crashes<br></font><br>
The parameters changed at some point this year, but the main <br>documentation link is still for 1.4-3. We now have the nightly build <br>documentation linked from the download page, e.g.:<br><br><span><a target="_blank" href="http://www.phenix-online.org/documentation/nightlies/1.4-147/automr.htm">http://www.phenix-online.org/documentation/nightlies/1.4-147/automr.htm</a></span><br><br>I suspect in this case it will be necessary to write a parameter file <br>rather than use the command line. Fortunately, there is a very good <br>example of this in the documentation.<br><br>On Sep 10, 2009, at 9:44 AM, Randy Read wrote:<br><br>> Did you cut and paste the command or retype it? If that's the exact <br>> command, I don't know what would be wrong with the bit <br>> "ensemble_1.coords=a1.pdb", but "ensemble_1_copies_to_find" should <br>> be "ensemble_1.copies_to_find" and "componenet"
should be <br>> "component" and "_mass" should be ".mass". So I wonder if the <br>> parser got confused by the other syntax errors?<br>><br>> Regards,<br>><br>> Randy Read<br>><br>> On 10 Sep 2009, at 17:28, r n wrote:<br>><br>>> Hi all<br>>><br>>> I am trying to use phenix.automr to search for two component.<br>>><br>>> Tried command line...<br>>><br>>> phenix.automr data=out.sca ensemble_1.coords=a1.pdb \<br>>> ensemble_1.RMS=0.65 ensemble_1_copies_to_find=5 <br>>> componenet_1_mass=25000 \<br>>> component_1.component_copies=5 ensemble_2.coords=a2.pdb \<br>>> ensemble_2.RMS=0.60 ensemble_2.copies_to_find=5 <br>>> componenet_2_mass=20000 \<br>>> component_2.component_copies=5<br>>><br>>> Following errors<br>>><br>>>
phenix-installer-1.4-147/phenix-1.4-147/phenix/phenix/command_line/ <br>>> <a target="_blank" href="http://automr.py">automr.py</a>", line 483, in <module><br>>> run_automr=run_automr(args=sys.argv[1:])<br>>> phenix-installer-1.4-147/phenix-1.4-147/phenix/phenix/autosol/ <br>>> <a target="_blank" href="http://wizard_command_line.py">wizard_command_line.py</a>", line 1237, in Sorry<br>>> raise AssertionError,e<br>>> AssertionError: Sorry, unknown file or keyword: <br>>> ensemble_1.coords=a1.pdb<br>>><br>>> Not sure , What is wrong in my command?<br>>><br>>> Also try to use the Gui, but in automr gui only seen option for <br>>> data file , not for model? May I am<br>>> missing something?<br>>><br>>> Thanks<br>>><br>>><br>>><br>>><br>>> _______________________________________________<br>>>
phenixbb mailing list<br>>> <a ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><span>>> <a target="_blank" href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a></span><br>><br>> ------<br>> Randy J. Read<br>> Department of Haematology, University of Cambridge<br>> Cambridge Institute for Medical Research Tel: + 44 1223 336500<br>> Wellcome Trust/MRC Building Fax: + 44 1223 336827<br>> Hills Road E-mail: <a ymailto="mailto:rjr27@cam.ac.uk" href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a><br>> Cambridge CB2 0XY, U.K.
www- <br>> <a target="_blank" href="http://structmed.cimr.cam.ac.uk">structmed.cimr.cam.ac.uk</a><br>><br>> _______________________________________________<br>> phenixbb mailing list<br>> <a ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>> <a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br><br>-------------------<br>Nathaniel Echols<br>Lawrence Berkeley Lab<br>510-486-5136<br><a ymailto="mailto:NEchols@lbl.gov" href="mailto:NEchols@lbl.gov">NEchols@lbl.gov</a><br><br><br><br>_______________________________________________<br>phenixbb mailing list<br><a ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb"
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