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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Apr 16, 2018 at 12:42 PM, Shintaro Aibara < [email protected]> 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 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 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::Job Distributor::run_one_job(std::shared_ptrprotocols::moves::Mover&, long, std::__cxx11::basic_string&, std::__cxx11::basic_string&, 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::Job Distributor::go_main(std::shared_ptrprotocols::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::Fil eSystemJobDistributor::go(std::shared_ptrprotocols::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/rosett a/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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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. Good luck Ursula On Tue, Apr 17, 2018 at 2:16 AM, Shintaro Aibara < [email protected]> wrote:

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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Apr 16, 2018 at 12:42 PM, Shintaro Aibara < [email protected]> 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_2018.09.600 72_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 const&, int)+0x2ea) [0x7f3e2b7798fa] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.600 72_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_2018.09.600 72_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 const&)+0x20a) [0x7f3e34c1771a] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.600 72_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_2018.09.600 72_bundle/main/source/build/src/release/linux/4.15/64/x86/ gcc/5.4/default/libprotocols.1.so(protocols::jd2::JobDistri butor::run_one_job(std::shared_ptrprotocols::moves::Mover&, long, std::__cxx11::basic_string&, std::__cxx11::basic_string&, unsigned long&, unsigned long&, bool)+0xbed) [0x7f3e344cc9bd] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.600 72_bundle/main/source/build/src/release/linux/4.15/64/x86/ gcc/5.4/default/libprotocols.1.so(protocols::jd2::JobDistri butor::go_main(std::shared_ptrprotocols::moves::Mover)+0x166) [0x7f3e344cedc6] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.600 72_bundle/main/source/build/src/release/linux/4.15/64/x86/ gcc/5.4/default/libprotocols.1.so(protocols::jd2::FileSyste mJobDistributor::go(std::shared_ptrprotocols::moves::Mover)+0x57) [0x7f3e344b4d67] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.600 72_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x40480e] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.600 72_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_2018.09.600 72_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4045b9] Traceback (most recent call last): File "/home/saibara/software/phenix/phenix-dev-3092/build/../modu les/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_2018.09.60 072_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_2018.09.60 072_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_2018.09.60 072_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/rosett a/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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-- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491