Dear PHENIX and ERRASER developers,

While ERRASER is running fine (command line) when I use a small PDB file, it fails repeatedly on a complete ribosome model giving following error:

Starting erraser

Date: Tue May  9 17:53:20 2017 

Directory: /home/tofayel/Desktop/test

HOSTNAME: localhost.localdomain

Log file will be /home/tofayel/Desktop/test/erraser.log 

Splitting output to  /home/tofayel/Desktop/test/erraser.log

Running ERRASER Rosetta app...

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

Path to ERRASER: /usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER

ERROR: Unique best command line context option match not found for -fixed_res.

Possible matches include:

-willmatch:fixed_res

-stepwise:fixed_res

-rna:farna:erraser:fixed_res

Either specify namespace from command line; or in code, use add_relevant() to register option.

Traceback (most recent call last):

  File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/erraser.py", line 14, in <module>

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

  File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 349, in __init__

    self.run(params,out=out)

  File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 459, in run

    erraser(option)

  File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 92, in erraser

    full_struct_slice_and_minimize( minimize_option )

  File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 662, in full_struct_slice_and_minimize

    erraser_minimize( minimize_option )

  File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 488, in erraser_minimize

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

  File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_util.py", line 101, in subprocess_call

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

  File "/usr/local/phenix-1.11.1-2575/base/lib/python2.7/subprocess.py", line 540, in check_call

    raise CalledProcessError(retcode, cmd)

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

Please suggest some fixes. Thanks in advanced.

Best regards,

Tofayel

    

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org