[phenixbb] ERRASER fails to run on ribosome model

[Nigel Moriarty]

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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