<div dir="ltr">The ERRASER people are working on this bug related to -fixed_res.</div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, May 10, 2017 at 7:37 PM, #AHMED TOFAYEL# <span dir="ltr"><<a href="mailto:TOFAYEL001@e.ntu.edu.sg" target="_blank">TOFAYEL001@e.ntu.edu.sg</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div><span style="color:rgb(0,111,201)">Dear PHENIX and ERRASER developers,</span></div>
<div><br>
</div>
<div><span style="color:rgb(0,111,201)">While ERRASER is running fine (command line</span><span style="color:rgb(0,111,201)">) </span><span style="color:rgb(0,111,201)">when I use a small PDB file, it fails</span><span style="color:rgb(0,111,201)"> repeatedly </span><span style="color:rgb(0,111,201)">on
a complete ribosome model giving following error:</span></div>
<div><br>
</div>
<div>Starting erraser</div>
<div>Date: Tue May 9 17:53:20 2017 </div>
<div>Directory: /home/tofayel/Desktop/test</div>
<div><br>
</div>
<div>HOSTNAME: localhost.localdomain</div>
<div>Log file will be /home/tofayel/Desktop/test/<wbr>erraser.log </div>
<div>Splitting output to /home/tofayel/Desktop/test/<wbr>erraser.log</div>
<div>Running ERRASER Rosetta app...</div>
<div>##############################<wbr>#####</div>
<div>Path to ERRASER: /usr/local/rosetta_src_2016.<wbr>32.58837_bundle/tools/ERRASER</div>
<div>ERROR: Unique best command line context option match not found for -fixed_res.</div>
<div>Possible matches include:</div>
<div><span class="m_332107662631459576Apple-tab-span" style="white-space:pre-wrap"></span>-willmatch:fixed_res</div>
<div><span class="m_332107662631459576Apple-tab-span" style="white-space:pre-wrap"></span>-stepwise:fixed_res</div>
<div><span class="m_332107662631459576Apple-tab-span" style="white-space:pre-wrap"></span>-rna:farna:erraser:fixed_res</div>
<div>Either specify namespace from command line; or in code, use add_relevant() to register option.</div>
<div><br>
</div>
<div>Traceback (most recent call last):</div>
<div> File "/usr/local/phenix-1.11.1-<wbr>2575/build/../modules/phenix/<wbr>phenix/command_line/erraser.<wbr>py", line 14, in <module></div>
<div> erraser_run=phenix.erraser.<wbr>erraser.erraser(args=sys.argv[<wbr>1:])</div>
<div> File "/usr/local/phenix-1.11.1-<wbr>2575/modules/phenix/phenix/<wbr>erraser/erraser.py", line 349, in __init__</div>
<div> self.run(params,out=out)</div>
<div> File "/usr/local/phenix-1.11.1-<wbr>2575/modules/phenix/phenix/<wbr>erraser/erraser.py", line 459, in run</div>
<div> erraser(option)</div>
<div> File "/usr/local/rosetta_src_2016.<wbr>32.58837_bundle/tools/ERRASER/<wbr>erraser_wrapper.py", line 92, in erraser</div>
<div> full_struct_slice_and_<wbr>minimize( minimize_option )</div>
<div> File "/usr/local/rosetta_src_2016.<wbr>32.58837_bundle/tools/ERRASER/<wbr>erraser_wrapper.py", line 662, in full_struct_slice_and_minimize</div>
<div> erraser_minimize( minimize_option )</div>
<div> File "/usr/local/rosetta_src_2016.<wbr>32.58837_bundle/tools/ERRASER/<wbr>erraser_wrapper.py", line 488, in erraser_minimize</div>
<div> subprocess_call(command, sys.stdout, sys.stderr)</div>
<div> File "/usr/local/rosetta_src_2016.<wbr>32.58837_bundle/tools/ERRASER/<wbr>erraser_util.py", line 101, in subprocess_call</div>
<div> subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)</div>
<div> File "/usr/local/phenix-1.11.1-<wbr>2575/base/lib/python2.7/<wbr>subprocess.py", line 540, in check_call</div>
<div> raise CalledProcessError(retcode, cmd)</div>
<div>subprocess.CalledProcessError: Command '/usr/local/rosetta_src_2016.<wbr>32.58837_bundle/main/source/<wbr>bin/erraser_minimizer.<wbr>linuxgccrelease -database /usr/local/rosetta_src_2016.<wbr>32.58837_bundle/main/database/ -s /home/tofayel/Desktop/test/<wbr>test-model-coot-19_erraser_<wbr>temp/minimize_0_full_minimize_<wbr>temp/before_min_temp_rs.pdb
-score:weights stepwise/rna/rna_hires_elec_<wbr>dens_FCC2012 -score:rna_torsion_potential FCC2012_RNA11_based_new -rna::corrected_geo true -rna::rna_prot_erraser false -rna::vary_geometry true -constrain_P true -attempt_pyrimidine_flip false -rna:farna:erraser:skip_<wbr>minimize
false -chemical:enlarge_H_lj false -in:guarantee_no_DNA false -scale_d 100 -scale_theta 10 -stepwise:rna:o2prime_legacy_<wbr>mode true -use_2prime_OH_potential false -fixed_res 78 79 100 101 102 106 107 108 109 110 115 116 -edensity:mapfile /home/tofayel/Desktop/test/<wbr>test-map.ccp4
-edensity:mapreso 3.3 -edensity:realign no -graphics false -skip_connect_info true ' returned non-zero exit status 255</div>
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<p><span style="color:rgb(0,111,201)">Please suggest some fixes. Thanks in advanced.</span></p>
<p><br>
</p>
<div id="m_332107662631459576Signature"><span style="color:rgb(0,111,201)"></span><span style="color:rgb(0,111,201)"></span>
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<p style="color:rgb(0,0,0)"><span style="color:rgb(0,111,201)">Best regards,</span></p>
<span style="color:rgb(0,111,201)"></span>
<p style="color:rgb(0,0,0)"><span style="color:rgb(0,111,201)">Tofayel</span></p>
<span style="color:rgb(0,111,201)"></span>
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<p style="color:rgb(0,0,0)"><span style="font-size:12pt"> </span><br>
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<p style="color:rgb(0,0,0)"><span style="font-size:12pt"></span></p>
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