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I’m using “rosetta_src_2017.36.59679_bundle”. I’m trying to run the following bash script:
#!/bin/bash
$ROSETTA3/home/labusr/rosetta/main/source/bin/score_jd2.macosclangrelease
-database $ROSETTA3/database/
-database ~/Rosetta/database/
-in::file:
/home/labusr/Documents/1issA.pdb
-ignore_unrecognized_res
-edensity::mapfile /home/labusr/Documents/1issA_6A.mrc
-edensity::mapreso 5.0
-edensity::grid_spacing 2.0
-edensity::fastdens_wt 35.0
-beta
-edensity::cryoem_scatterers
-crystal_refineI get “No such file or directory” and indeed I don’t have that file. What I have is:
score_aln2.linuxgccrelease
score_aln.default.linuxgccrelease
score_aln.linuxgccrelease
score.default.linuxgccrelease
score_jd2.default.linuxgccrelease
score_jd2.linuxgccrelease
score.linuxgccrelease
And trying score_jd2.default.linuxgccrelease or score_jd2.linuxgccrelease gives me the error below. How can I fix it?
core.init: Rosetta version rosetta.source.release-152:d6547f6858282e67c41356255dfdd63b0e7a75aa 2017-09-08 02:01:37.594540 from http://www.rosettacommons.org
core.init: command: /home/labusr/rosetta/main/source/bin/score.linuxgccrelease -database /database/ -database /home/labusr/Rosetta/database/ -in::file: /home/labusr/Documents/1issA.pdb -ignore_unrecognized_res -edensity::mapfile /home/labusr/Documents/1issA_6A.mrc -edensity::mapreso 5.0 -edensity::grid_spacing 2.0 -edensity::fastdens_wt 35.0 -beta -edensity::cryoem_scatterers -crystal_refine
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=289470737 seed_offset=0 real_seed=289470737
core.init.random: RandomGenerator:init: Normal mode, seed=289470737 RG_type=mt19937
Rosetta Tool: score - rescores PDBs and silent files, extracts PDBs from silent files, assembles PDBs into silent files.
Usage:
PDB input: -in:file:s *.pdb or
-in:file:l list_of_pdbs
-no_optH Dont change positions of Hydrogen atoms! (default true, specify false if you want optH)
Silent input: -in:file:silent silent.out silent input filesname
-in:file:tags specify specific tags to be extracted, if left out all will be taken
-in:file:fullatom for full atom structures
-in:file:binary_silentfile for non-ideal structures (such as from looprelax)
-in:file:silent_optH Call optH when reading silent files (useful for HisD/HisE determination)
-score_app:linmin Run a quick linmin before scoring
Native: -in:file:native native PDB (rms, maxsub and gdtm scores will be calculated)
Scorefunction: -score:weights weights weight set or weights file
-score:patch patch patch set
-score:optH_weights Weights file for optH (default standard.wts w/ sc12 patch)
-score:optH_patch Weights patch file for optH
-rescore:verbose display score breakdown
Output: -out:nooutput don't print PDB structures (default now)
-out:output force printing of PDB structures
-out:file:silent write silent-out file
-out:file:scorefile name write scorefile (default default.sc)
-out:prefix myprefix prefix the output structures with a string
Examples:
score -database ~/minirosetta_database -in:file:silent silent.out -in::file::binary_silentfile -in::file::fullatom -native 1a19.pdb
Will rescore all structures in silent.out, in full atom mode and accounting for nonideal structure if present. Additionally
it will print a PDB for every structure with -out:output flag
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_nov16.wts
ERROR: Unable to open weights/patch file. None of (./)beta_nov16.wts or (./)beta_nov16.wts.wts or /database/scoring/weights/beta_nov16.wts or /database/scoring/weights/beta_nov16.wts.wts exist
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 2727
BACKTRACE:
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x27f) [0x7fcad925348f]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::scoring::find_weights_file(std::string, std::string)+0x7e2) [0x7fcadb6ea002]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::scoring::ScoreFunction::add_weights_from_file(std::string const&)+0x4c) [0x7fcadb6f953c]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::scoring::ScoreFunctionFactory::create_score_function(utility::options::OptionCollection const&, std::string const&, utility::vector1<std::string, std::allocator<std::string> > const&)+0x24d) [0x7fcadb71db5d]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::scoring::ScoreFunctionFactory::create_score_function(std::string const&, utility::vector1<std::string, std::allocator<std::string> > const&)+0x16) [0x7fcadb71e506]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::scoring::get_score_function(utility::options::OptionCollection const&, bool)+0x6c4) [0x7fcadb71ebd4]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::scoring::get_score_function(bool)+0x14) [0x7fcadb71f424]
/home/labusr/rosetta/main/source/bin/score.linuxgccrelease() [0x40c2ec]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7fcad7248c05]
/home/labusr/rosetta/main/source/bin/score.linuxgccrelease() [0x40d754]
caught exception
[ ERROR ] EXCN_utility_exit has been thrown from: src/core/scoring/ScoreFunction.cc line: 2727
ERROR: Unable to open weights/patch file. None of (./)beta_nov16.wts or (./)beta_nov16.wts.wts or /database/scoring/weights/beta_nov16.wts or /database/scoring/weights/beta_nov16.wts.wts exist
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