<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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?<div><br></div><div>Regards,</div><div><br></div><div>Randy Read</div><div><br><div><div>On 10 Sep 2009, at 17:28, r n wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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 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 componenet_2_mass=20000 \<br>component_2.component_copies=5<span class="Apple-converted-space"> </span><br><br>Following errors<br><br>phenix-installer-1.4-147/phenix-1.4-147/phenix/phenix/command_line/automr.py", 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/wizard_command_line.py", line 1237, in Sorry<br> raise AssertionError,e<br>AssertionError: Sorry, unknown file or keyword: ensemble_1.coords=a1.pdb<br><br>Not sure , What is wrong in my command?<span class="Apple-converted-space"> </span><br><br>Also try to use the Gui, but in automr gui only seen option for data file , not for model? May I am<br>missing something?<br><br>Thanks<br><br><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><a ymailto="mailto:1476.152.1.132.71.1252513056.squirrel@webmail.ncsu.edu" href="mailto:1476.152.1.132.71.1252513056.squirrel@webmail.ncsu.edu"></a><br></div></div><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></div></span></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div>------</div><div>Randy J. Read</div><div>Department of Haematology, University of Cambridge</div><div>Cambridge Institute for Medical Research Tel: + 44 1223 336500</div><div>Wellcome Trust/MRC Building Fax: + 44 1223 336827</div><div>Hills Road E-mail: <a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a></div><div>Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk</div></span></div></span> </div><br></div></body></html>