<div dir="ltr"><div><div>I used Erraser fairly recently in Phenix 1.12_2829 using the command line. It worked fine from the command line, but I also had no success from the GUI.<br><br></div>Good luck<br><br></div>Ursula<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Apr 17, 2018 at 2:16 AM, Shintaro Aibara <span dir="ltr">&lt;<a href="mailto:shintaro.aibara@scilifelab.se" target="_blank">shintaro.aibara@scilifelab.se</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Nigel,<div><br></div><div>Thanks for letting me know. Are there any previous versions of Phenix/Rosetta that are known to work? I remember getting it to run on OSX in the past at some point....It would be great if I could run some jobs even if it means running it through the command-line</div><div><br></div><div>Best wishes,</div><div>Shintaro</div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Apr 16, 2018 at 11:38 PM, Nigel Moriarty <span dir="ltr">&lt;<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Shintaro<div><br></div><div>The ERRASER interface is a little broken. We are working on it and will make an announcement when it&#39;s fixed.</div><div><br></div><div>Sorry.</div></div><div class="gmail_extra"><br clear="all"><div><div class="m_8029921412261974415m_8232461048087332639gmail_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"><div><div class="m_8029921412261974415h5">On Mon, Apr 16, 2018 at 12:42 PM, Shintaro Aibara <span dir="ltr">&lt;<a href="mailto:shintaro.aibara@scilifelab.se" target="_blank">shintaro.aibara@scilifelab.se</a><wbr>&gt;</span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="m_8029921412261974415h5"><div dir="ltr"><b>Dear PhenixBB,</b><div><b><br></b></div><div><b>I am trying to get ERRASER to run and am struggling a bit. I was wondering if somebody could point me in the right way. Apologies if this has been asked before - my Google-Fu is inadequate.</b></div><div><b><br></b></div><div><b>Phenix Version: dev-3092</b></div><div><b>Rosetta Version: 2018.09.60072</b></div><div><b><br></b></div><div><b>I built rosetta using scons as per the instructions online and fired rosetta.build_phenix_interface with no errors. I&#39;ve identified that the erraser directory lives in main/source/src/apps/public/ER<wbr>RASER and accordingly set my environmental variables.</b></div><div><b><br></b></div><div><b>Being fairly clunky around the linux environment, I am probably doing something very silly. Any help would be much appreciated.</b></div><div><b><br></b></div><div><b>Best wishes,</b></div><div><b>Shintaro</b></div><div><b><br></b></div><div><b>When I try to run erraser from the phenix GUI I am greeted by this error message:</b></div><div><div><br></div><div>TypeError : __init__() takes at least 3 arguments (1 given)</div><div><br></div><div>Traceback (most recent call last):</div><div>  File &quot;/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/pheni<wbr>x/wxGUI2/App.py&quot;, line 784, in OnTimer</div><div>    self.run_manager.update(update<wbr>_backgrounded=False)</div><div>  File &quot;/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/pheni<wbr>x/wxGUI2/ProcessControl.py&quot;, line 213, in update</div><div>    process.update()</div><div>  File &quot;/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/pheni<wbr>x/wxGUI2/ProcessControl.py&quot;, line 136, in update</div><div>    self._process.update()</div><div>  File &quot;/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/cctbx<wbr>_project/libtbx/runtime_utils.<wbr>py&quot;, line 306, in update</div><div>    (error, traceback_info) = easy_pickle.load(self.error_fi<wbr>le)</div><div>  File &quot;/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/cctbx<wbr>_project/libtbx/easy_pickle.<wbr>py&quot;, line 80, in load</div><div>    return cPickle.loads(_open(file_name, &quot;rb&quot;).read())</div><div>TypeError: __init__() takes at least 3 arguments (1 given)</div></div><div><br></div><div><br></div><div><b>Alternatively if I try to fire phenix.erraser through the command line, I get something like this:</b></div><div><br></div><div><div>Running ERRASER Rosetta app...</div><div>##############################<wbr>#####</div><div>Path to ERRASER: /home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/src/apps<wbr>/public/ERRASER</div><div><br></div><div>ERROR: Assertion `scorefxn_-&gt;get_weight( cart_bonded ) &gt; 0` failed.</div><div>ERROR:: Exit from: src/protocols/rna/movers/Erras<wbr>erMinimizerMover.cc line: 238</div><div>BACKTRACE:</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/build/<wbr>src/release/linux/4.15/64/x86/<wbr>gcc/5.4/default/libutility.so(<wbr>utility::exit(char const*, int, std::__cxx11::basic_string&lt;cha<wbr>r, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt; const&amp;, int)+0x2ea) [0x7f3e2b7798fa]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/build/<wbr>src/release/linux/4.15/64/x86/<wbr>gcc/5.4/default/<a href="http://libprotocols_d.6.so" target="_blank">libprotocols_<wbr>d.6.so</a>(protocols::rna::movers:<wbr>:ErraserMinimizerMover::i_<wbr>want_this_atom_to_move(core::<wbr>chemical::ResidueType const&amp;, unsigned long const&amp;)+0x92) [0x7f3e34c17062]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/build/<wbr>src/release/linux/4.15/64/x86/<wbr>gcc/5.4/default/<a href="http://libprotocols_d.6.so" target="_blank">libprotocols_<wbr>d.6.so</a>(protocols::rna::movers:<wbr>:ErraserMinimizerMover::vary_<wbr>bond_geometry(core::kinematics<wbr>::MoveMap&amp;, core::pose::Pose&amp;, ObjexxFCL::FArray1D&lt;bool&gt;&amp;, std::set&lt;unsigned long, std::less&lt;unsigned long&gt;, std::allocator&lt;unsigned long&gt; &gt; const&amp;)+0x20a) [0x7f3e34c1771a]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/build/<wbr>src/release/linux/4.15/64/x86/<wbr>gcc/5.4/default/<a href="http://libprotocols_d.6.so" target="_blank">libprotocols_<wbr>d.6.so</a>(protocols::rna::movers:<wbr>:ErraserMinimizerMover::apply(<wbr>core::pose::Pose&amp;)+0x2020) [0x7f3e34c20f70]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/build/<wbr>src/release/linux/4.15/64/x86/<wbr>gcc/5.4/default/<a href="http://libprotocols.1.so" target="_blank">libprotocols.<wbr>1.so</a>(protocols::jd2::JobDistri<wbr>butor::run_one_job(std::shared<wbr>_ptr&lt;protocols::moves::Mover&gt;&amp;<wbr>, long, std::__cxx11::basic_string&lt;cha<wbr>r, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt;&amp;, std::__cxx11::basic_string&lt;cha<wbr>r, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt;&amp;, unsigned long&amp;, unsigned long&amp;, bool)+0xbed) [0x7f3e344cc9bd]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/build/<wbr>src/release/linux/4.15/64/x86/<wbr>gcc/5.4/default/<a href="http://libprotocols.1.so" target="_blank">libprotocols.<wbr>1.so</a>(protocols::jd2::JobDistri<wbr>butor::go_main(std::shared_<wbr>ptr&lt;protocols::moves::Mover&gt;)+<wbr>0x166) [0x7f3e344cedc6]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/build/<wbr>src/release/linux/4.15/64/x86/<wbr>gcc/5.4/default/<a href="http://libprotocols.1.so" target="_blank">libprotocols.<wbr>1.so</a>(protocols::jd2::FileSyste<wbr>mJobDistributor::go(std::<wbr>shared_ptr&lt;protocols::moves::M<wbr>over&gt;)+0x57) [0x7f3e344b4d67]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/bin/erra<wbr>ser_minimizer.linuxgccrelease(<wbr>) [0x40480e]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/bin/erra<wbr>ser_minimizer.linuxgccrelease(<wbr>) [0x4037b1]</div><div>/lib/x86_64-linux-gnu/libc.so.<wbr>6(__libc_start_main+0xf0) [0x7f3e32bdc830]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/source/bin/erra<wbr>ser_minimizer.linuxgccrelease(<wbr>) [0x4045b9]</div><div>Traceback (most recent call last):</div><div>  File &quot;/home/saibara/software/phenix<wbr>/phenix-dev-3092/build/../modu<wbr>les/phenix/phenix/command_line<wbr>/erraser.py&quot;, line 14, in &lt;module&gt;</div><div>    erraser_run=phenix.erraser.err<wbr>aser.erraser(args=sys.argv[1:]<wbr>)</div><div>  File &quot;/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/pheni<wbr>x/phenix/erraser/erraser.py&quot;, line 349, in __init__</div><div>    self.run(params,out=out)</div><div>  File &quot;/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/pheni<wbr>x/phenix/erraser/erraser.py&quot;, line 459, in run</div><div>    erraser(option)</div><div>  File &quot;/home/saibara/software/rosett<wbr>a/rosetta_bin_linux_2018.09.60<wbr>072_bundle/main/source/src/app<wbr>s/public/ERRASER/erraser_wrapp<wbr>er.py&quot;, line 99, in erraser</div><div>    erraser_minimize( minimize_option ) #full_struct_slice_and_minimiz<wbr>e( minimize_option )</div><div>  File &quot;/home/saibara/software/rosett<wbr>a/rosetta_bin_linux_2018.09.60<wbr>072_bundle/main/source/src/app<wbr>s/public/ERRASER/erraser_wrapp<wbr>er.py&quot;, line 478, in erraser_minimize</div><div>    subprocess_call(command, sys.stdout, sys.stderr)</div><div>  File &quot;/home/saibara/software/rosett<wbr>a/rosetta_bin_linux_2018.09.60<wbr>072_bundle/main/source/src/app<wbr>s/public/ERRASER/erraser_util.<wbr>py&quot;, line 107, in subprocess_call</div><div>    subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)</div><div>  File &quot;/home/saibara/software/phenix<wbr>/phenix-dev-3092/base/lib/pyth<wbr>on2.7/subprocess.py&quot;, line 186, in check_call</div><div>    raise CalledProcessError(retcode, cmd)</div><div>subprocess.CalledProcessError: Command &#39;/home/saibara/software/rosett<wbr>a/rosetta_bin_linux_2018.09.60<wbr>072_bundle/main/source/bin/err<wbr>aser_minimizer.linuxgccrelease -database /home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.600<wbr>72_bundle/main/database/  -s /home/saibara/Phenix/hsmitorib<wbr>o_drug/rnaonly_erraser_temp/mi<wbr>nimize_0.pdb  -score:weights stepwise/rna/rna_hires_elec_de<wbr>ns_FCC2012   -score:rna_torsion_potential FCC2012_RNA11_based_new  -rna::corrected_geo true  -rna::erraser::rna_prot_errase<wbr>r false  -rna::vary_geometry true  -constrain_P true  -attempt_pyrimidine_flip false  -rna::erraser::skip_minimize false  -chemical:enlarge_H_lj false  -in:guarantee_no_DNA false  -out:file:write_pdb_link_recor<wbr>ds true  -scale_d 100  -scale_theta 10  -stepwise:rna:o2prime_legacy_m<wbr>ode true  -use_2prime_OH_potential false  -edensity:mapfile /home/saibara/Phenix/hsmitorib<wbr>o_drug/cheatmap.ccp4  -edensity:mapreso 3.0  -edensity:realign no  -graphics false  -skip_connect_info true &#39; returned non-zero exit status 255</div></div><div><br></div></div>
<br></div></div>______________________________<wbr>_________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailm<wbr>an/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.o<wbr>rg</a><br></blockquote></div><br></div>
</blockquote></div><br></div>
</div></div><br>______________________________<wbr>_________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.<wbr>org</a><br></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Ursula Schulze-Gahmen, Ph.D.<br>Project Scientist<br>UC Berkeley, QB3<br>360 Stanley Hall #3220<br>Berkeley, CA 94720-3220<br>(510) 643 9491<br></div></div>
</div>