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<p class=MsoNormal><span lang=EN-US style='font-family:"Arial","sans-serif"'>Hi,
everyone<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Arial","sans-serif"'>I
have a problem in running phenix.automr<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Arial","sans-serif"'>I
started AutoMR with the command:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>---------------------------------------------------------------------------------<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>phenix.automr
build=True data=ZZZZZZ_H-Nat_x22_P3221_from_P321.sca \<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>coords='1_SMsp.pdb
2_SMsp.pdb 3_SMsp.pdb 4_SMsp.pdb' \<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>identity='40
32 29 27' seq_file=ZZZZZZ_seq.dat input_seq_file=ZZZZZZ_seq.dat \<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>copies=4<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>----------------------------------------------------------------------------------<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Arial","sans-serif"'>AutoMR
process seems to be done without any error<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Arial","sans-serif"'>but
during autobuild process, I encounterd an error message as follows<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>---------------------------------------------------------------------------------<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Re-using
input PDB coordinates in build this cycle<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Running
3 parallel build jobs<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Standard
build in parallel starting with refine.pdb_1<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>This is
the first try at building this model<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Setting
background=False as nproc=1<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Try:
1 building 1 model<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Try:
2 building 1 model<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Try:
3 building 1 model<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Running
up to 1 jobs in parallel... with total of 3 jobs<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Splitting
work into 3 jobs and running 1 at a time with csh in<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>/data1/disk02/icshin/UGI/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'>Starting
job 1...<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New";
color:red'>********************************************************************************<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New";
color:red'>Failed to carry out AutoBuild_build_cycle:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New";
color:red'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New";
color:red'>child process stderr output:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New";
color:red'> command: 'csh
/data1/disk02/icshin/ZZZ/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0/RUN_FILE_1'<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New";
color:red'> icshin_com: No such file or directory.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-family:"Courier New";
color:red'>********************************************************************************<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>--------------------------------------------------------------------------------------------------------------------------------------<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>What am I supposed to do? Please, help me!<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><b><span lang=EN-US style='font-family:±¼¸²'>-------------------------------------------------------<o:p></o:p></span></b></p>
<p class=MsoNormal><b><span lang=EN-US style='font-family:±¼¸²'>Inchul Shin<o:p></o:p></span></b></p>
<p class=MsoNormal><b><span lang=EN-US style='font-family:±¼¸²'>Structural
Biology Lab. CALS. Seoul Nationl Univ.<o:p></o:p></span></b></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
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