<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif;" dir="ltr">
<p></p>
<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/erraser.log </div>
<div>Splitting output to /home/tofayel/Desktop/test/erraser.log</div>
<div>Running ERRASER Rosetta app...</div>
<div>###################################</div>
<div>Path to ERRASER: /usr/local/rosetta_src_2016.32.58837_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="Apple-tab-span" style="white-space:pre"></span>-willmatch:fixed_res</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>-stepwise:fixed_res</div>
<div><span class="Apple-tab-span" style="white-space:pre"></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-1.11.1-2575/build/../modules/phenix/phenix/command_line/erraser.py", line 14, in <module></div>
<div> erraser_run=phenix.erraser.erraser.erraser(args=sys.argv[1:])</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 349, in __init__</div>
<div> self.run(params,out=out)</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 459, in run</div>
<div> erraser(option)</div>
<div> File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 92, in erraser</div>
<div> full_struct_slice_and_minimize( minimize_option )</div>
<div> File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 662, in full_struct_slice_and_minimize</div>
<div> erraser_minimize( minimize_option )</div>
<div> File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 488, in erraser_minimize</div>
<div> subprocess_call(command, sys.stdout, sys.stderr)</div>
<div> File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/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-1.11.1-2575/base/lib/python2.7/subprocess.py", line 540, in check_call</div>
<div> raise CalledProcessError(retcode, cmd)</div>
<div>subprocess.CalledProcessError: Command '/usr/local/rosetta_src_2016.32.58837_bundle/main/source/bin/erraser_minimizer.linuxgccrelease -database /usr/local/rosetta_src_2016.32.58837_bundle/main/database/ -s /home/tofayel/Desktop/test/test-model-coot-19_erraser_temp/minimize_0_full_minimize_temp/before_min_temp_rs.pdb
-score:weights stepwise/rna/rna_hires_elec_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_minimize
false -chemical:enlarge_H_lj false -in:guarantee_no_DNA false -scale_d 100 -scale_theta 10 -stepwise:rna:o2prime_legacy_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/test-map.ccp4
-edensity:mapreso 3.3 -edensity:realign no -graphics false -skip_connect_info true ' returned non-zero exit status 255</div>
<br>
<p></p>
<p><span style="color: rgb(0, 111, 201);">Please suggest some fixes. Thanks in advanced.</span></p>
<p><br>
</p>
<div id="Signature"><span style="color: rgb(0, 111, 201);"></span><style type="text/css" style="display:none"><span style="color: rgb(0, 111, 201);"> <!-- p {margin-top:0; margin-bottom:0} --> </span></style><span style="color: rgb(0, 111, 201);"></span>
<div id="divtagdefaultwrapper" style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif; background-color:rgb(255,255,255)">
<span style="color: rgb(0, 111, 201);"></span>
<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>
<p style="color:rgb(0,0,0)"><br>
</p>
<p style="color:rgb(0,0,0)"><span style="font-size: 12pt;"> </span><br>
</p>
<p style="color:rgb(0,0,0)"></p>
<p style="color:rgb(0,0,0)"></p>
<p style="color:rgb(0,0,0)"><span style="font-size:12pt"></span></p>
</div>
</div>
</div>
</body>
</html>