Thank you Graeme. I have installed ccp4 6.1.1 and ran the same job on SCALA succesfully.
J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: [email protected] alternative email: [email protected] web page: ----- Original Message ---- From: Graeme Winter <[email protected]> To: James Foadi <[email protected]> Cc: [email protected] Sent: Tuesday, 24 February, 2009 18:51:16 Subject: Re: [ccp4bb] SCALA failed message Hi James, You are the victim of an epic command line. This has been fixed in the 6.1.1 release, but you will find that using a shorter path (i.e. noniso rather than non-isomorphism &c.) will pull the command line down to something more sensible. CCP4i writes this out to allow the job to be rerun in a comment, but the comment is too long for Scala! Cheers, Graeme 2009/2/24 James Foadi <[email protected]>: > Dear all, > I am running SCALA using ccp4i. The generated command file is: > > > ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > > ******************************************************************* > /tmp/james/NONISO_insulin_from_liz_6_2_com.tmp > ******************************************************************* > title Scale merged insulin_from_liz _ Datasets in1, in2, in3, in4, in5 > run 1 - > INCLUDE batch 1 to 100 > run 2 - > INCLUDE batch 201 to 380 > run 3 - > INCLUDE batch 401 to 522 > run 4 - > INCLUDE batch 601 to 651 > run 5 - > INCLUDE batch 701 to 720 > RUN 2 reference > name run 1 project New crystal New dataset New > name run 2 project New crystal New dataset New > name run 3 project New crystal New dataset New > name run 4 project New crystal New dataset New > name run 5 project New crystal New dataset New > exclude EMAX - > 10.0 > partials - > check - > test 0.95 1.05 - > nogap > intensities INTEGRATED - > PARTIALS > final PARTIALS > scales - > rotation SPACING 5 - > secondary 6 - > bfactor ON - > BROTATION SPACING 20 > UNFIX V > FIX A0 > UNFIX A1 > initial MEAN > tie surface 0.001 > tie bfactor 0.3 > cycles 10 converge 0.3 reject 2 > output AVERAGE > print brief nooverlap > RSIZE 80 > ## This script run with the command ########## > # /home/james/build/ccp4-6.1.0/bin/scala HKLIN > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/exp_01/in1_in2_in3_in4_in5_MS_1_001.mtz" > HKLOUT "/tmp/james/NONISO_insulin_from_liz_6_1_mtz.tmp" SCALES > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6.scala" > ROGUES > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogues.log" > NORMPLOT > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_normplot.xmgr" > ANOMPLOT > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_anomplot.xmgr" > PLOT > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_surface_plot.plt" > CORRELPLOT > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_correlplot.xmgr" > ROGUEPLOT > > "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogueplot.xmgr" > ################################################ > ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Unfortunately SCALA stops immediately with the following error message: > > > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > ** Unrecognized keyword ** > > **** RUN command must come before SCALES definition **** > > ** Missing or illegal value ** > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Any idea on what's wrong? I have to say, I had run this before with similar > data (up to 4 runs), and had never this problem. > > Thank you! > > J > > Dr James Foadi PhD > Membrane Protein Laboratory > Diamond Light Source Ltd. > Diamond House > Harwell Science and Innovation Campus > Didcot > Oxfordshire > OX11 0DE > United Kingdom > > > office email: [email protected] > alternative email: [email protected] > web page: > > > > >
