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<p class="MsoNormal">Hi all,<br>
</p>
<p class="MsoNormal">I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using:</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">phenix.mr_rosetta \</span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">seq_file = seq.dat \
</span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">data=coords1.mtz \<span style="">&nbsp;&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">search_models=coords1.pdb \<span style="">&nbsp;&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">run_prerefine=True \<span style="">&nbsp;&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">number_of_prerefine_models=1000 \<span style="">&nbsp;&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">fragment_files = test3.gz \<span style="">&nbsp;&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">fragment_files = test9.gz \<span style="">&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">rescore_mr.relax=False \<span style="">&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">rosetta_models=20 \<span style="">&nbsp;&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">space_group=p222<span style="">&nbsp;
</span>\<span style="">&nbsp;&nbsp; </span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">use_all_plausible_sg=False \<span style="">&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">nproc=4 \<span style="">&nbsp;&nbsp;
</span></span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">group_run_command=qsub\</span></p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><span style="font-size: 10pt; font-family: Courier;">&nbsp;</span></p>
<p class="MsoNormal">When I run the above script, it gives the following error message:</p>
<p class="MsoNormal">child process stderr output:</p>
<p class="MsoNormal"><span style="">&nbsp; </span>command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1'</p>
<p class="MsoNormal"><span style="">&nbsp; </span>/bin/sh: qsub: not found</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;">Then, I omit the last line in the command �<span style="font-size: 10pt; font-family: Courier;">group_run_command=qsub\</span>�. MR_ROSETTA seems to be running.<span style="">&nbsp;
</span>But, it takes forever to run. </p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;"><br>
</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;">My questions is:</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm 0.1pt 36pt; text-indent: -18pt;"><span style=""><span style="">1.<span style="font: 7pt &quot;Times New Roman&quot;;">&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span>Does anyone happen to know why it tells me �qsub: not found� when I include
<span style="">&nbsp;</span>�group_run_command=qsub� in my script?</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm 0.1pt 36pt; text-indent: -18pt;"><span style=""><span style="">2.<span style="font: 7pt &quot;Times New Roman&quot;;">&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span>When I omit �group_run_command=qsub� in the script, mr_rosetta seems to be running.<span style="">&nbsp; But
</span>it just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don�t know whether this is normal. If not, any idea about why it�s so slow and any suggestions about how to speed up the run? Thank you so much!<br>
</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm 0.1pt 36pt;">&nbsp;</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;">Splitting work into 1 jobs and running with 4 processors using sh
</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;">background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;">&nbsp;</p>
<p class="MsoNormal" style="margin: 0.1pt 0cm;">Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log</p>
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