Hi Nigel,

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

Best wishes,

Shintaro

On Mon, Apr 16, 2018 at 11:38 PM, Nigel Moriarty <nwmoriarty@lbl.gov> wrote:

Shintaro

The ERRASER interface is a little broken. We are working on it and will make an announcement when it's fixed.

Sorry.

Cheers

Nigel

---

Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging

Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Mon, Apr 16, 2018 at 12:42 PM, Shintaro Aibara <shintaro.aibara@scilifelab.se> wrote:

Dear PhenixBB,

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.

Phenix Version: dev-3092

Rosetta Version: 2018.09.60072

I built rosetta using scons as per the instructions online and fired rosetta.build_phenix_interface with no errors. I've identified that the erraser directory lives in main/source/src/apps/public/ERRASER and accordingly set my environmental variables.

Being fairly clunky around the linux environment, I am probably doing something very silly. Any help would be much appreciated.

Best wishes,

Shintaro

When I try to run erraser from the phenix GUI I am greeted by this error message:

TypeError : __init__() takes at least 3 arguments (1 given)

Traceback (most recent call last):

  File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/App.py", line 784, in OnTimer

    self.run_manager.update(update_backgrounded=False)

  File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py", line 213, in update

    process.update()

  File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py", line 136, in update

    self._process.update()

  File "/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/runtime_utils.py", line 306, in update

    (error, traceback_info) = easy_pickle.load(self.error_file)

  File "/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/easy_pickle.py", line 80, in load

    return cPickle.loads(_open(file_name, "rb").read())

TypeError: __init__() takes at least 3 arguments (1 given)

Alternatively if I try to fire phenix.erraser through the command line, I get something like this:

Running ERRASER Rosetta app...

###################################

Path to ERRASER: /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER

ERROR: Assertion `scorefxn_->get_weight( cart_bonded ) > 0` failed.

ERROR:: Exit from: src/protocols/rna/movers/ErraserMinimizerMover.cc line: 238

BACKTRACE:

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2ea) [0x7f3e2b7798fa]

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(core::chemical::ResidueType const&, unsigned long const&)+0x92) [0x7f3e34c17062]

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(core::kinematics::MoveMap&, core::pose::Pose&, ObjexxFCL::FArray1D<bool>&, std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > const&)+0x20a) [0x7f3e34c1771a]

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::apply(core::pose::Pose&)+0x2020) [0x7f3e34c20f70]

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xbed) [0x7f3e344cc9bd]

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x166) [0x7f3e344cedc6]

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x57) [0x7f3e344b4d67]

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x40480e]

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4037b1]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f3e32bdc830]

/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4045b9]

Traceback (most recent call last):

  File "/home/saibara/software/phenix/phenix-dev-3092/build/../modules/phenix/phenix/command_line/erraser.py", line 14, in <module>

    erraser_run=phenix.erraser.erraser.erraser(args=sys.argv[1:])

  File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py", line 349, in __init__

    self.run(params,out=out)

  File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py", line 459, in run

    erraser(option)

  File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 99, in erraser

    erraser_minimize( minimize_option ) #full_struct_slice_and_minimize( minimize_option )

  File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 478, in erraser_minimize

    subprocess_call(command, sys.stdout, sys.stderr)

  File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call

    subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)

  File "/home/saibara/software/phenix/phenix-dev-3092/base/lib/python2.7/subprocess.py", line 186, in check_call

    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command '/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease -database /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/database/  -s /home/saibara/Phenix/hsmitoribo_drug/rnaonly_erraser_temp/minimize_0.pdb  -score:weights stepwise/rna/rna_hires_elec_dens_FCC2012   -score:rna_torsion_potential FCC2012_RNA11_based_new  -rna::corrected_geo true  -rna::erraser::rna_prot_erraser 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_records true  -scale_d 100  -scale_theta 10  -stepwise:rna:o2prime_legacy_mode true  -use_2prime_OH_potential false  -edensity:mapfile /home/saibara/Phenix/hsmitoribo_drug/cheatmap.ccp4  -edensity:mapreso 3.0  -edensity:realign no  -graphics false  -skip_connect_info true ' returned non-zero exit status 255

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