[phenixbb] ERRASER fails to run on ribosome model
Nigel Moriarty
nwmoriarty at lbl.gov
Thu May 11 08:19:59 PDT 2017
The ERRASER people are working on this bug related to -fixed_res.
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 at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Wed, May 10, 2017 at 7:37 PM, #AHMED TOFAYEL# <TOFAYEL001 at e.ntu.edu.sg>
wrote:
> 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
>
>
>
>
>
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