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score_jd2.macosclangrelease No such file or directory

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score_jd2.macosclangrelease No such file or directory

I'm using "rosetta_src_2017.36.59679_bundle". I'm trying to run the following bash script:


$ROSETTA3/home/labusr/rosetta/main/source/bin/score_jd2.macosclangrelease \
 -database $ROSETTA3/database/ \
 -database ~/Rosetta/database/ \
 -in::file::s /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 \


I get "No such file or directory" and indeed I don't have that file. What I have is:


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
core.init: command: /home/labusr/rosetta/main/source/bin/score.linuxgccrelease -database /database/ -database /home/labusr/Rosetta/database/ -in::file::s /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. 
   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
                   -out:prefix  myprefix                       prefix the output structures with a string 
   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/ line: 2727
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/ 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/, std::string)+0x7e2) [0x7fcadb6ea002]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/ const&)+0x4c) [0x7fcadb6f953c]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/ 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/ 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/ const&, bool)+0x6c4) [0x7fcadb71ebd4]
/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/ [0x7fcadb71f424]
/home/labusr/rosetta/main/source/bin/score.linuxgccrelease() [0x40c2ec]
/lib64/ [0x7fcad7248c05]
/home/labusr/rosetta/main/source/bin/score.linuxgccrelease() [0x40d754]
caught exception 

[ ERROR ] EXCN_utility_exit has been thrown from: src/core/scoring/ 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


Post Situation: 
Mon, 2017-11-27 09:26

You're correct that the application to use for your platform (Linux, using a GCC compiler) is score_jd2.linuxgccrelease rather than score_jd2.macosclangrelease, which is what a person using the Clang compiler on MacOS would use. (Generally speaking, you'll often need to manually translate the extension of the application. -- Don't worry, they should function similarly.

Regarding the "Unable to open weights/patch file.", this is due to you having "-database /database/" on the commandline, which is there because $ROSETTA3 isn't set on your system. Rosetta is trying (and failing) to find the Rosetta database files in a directory named 'database' under the root of your filesystem -- it's highly likely that there isn't any such directory. Likewise, there likely isn't a  /home/labusr/Rosetta/database/ either.  Just like the other filenames, you would need to modify the paths in order to point to the correct location of the database on your system.

That said, if you compile in the directory you extracted Rosetta into, and you haven't done any moving around or re-arranging of the folders that Rosetta has, Rosetta these days frequently does a decent job of automatically finding the correct version of the database (that is, the one downloaded with the code). Frankly speaking, I'd recommend just omitting any `-database` options from your command line and options files, unless you are one of those small fraction who does wish to re-arrange the Rosetta directories.

Mon, 2017-11-27 09:56

Thanks. What you said does work, but since I'm a bit new to linux, how to set "dollar sign" ROSETTA3  to be recognized by my system. My guess is "dollar sign" ROSETTA3 is an environment variable with the rosetta path stored there? Can I just add the rosetta bath to my $PATH variable? 

Tue, 2017-11-28 09:05

You can write 

export ROSETTA3=/path/to/Rosetta/main

in your .bashrc.

Alternatively, explicitly give the Rosetta database directory like you're trying to do in the second line

 -database ~/Rosetta/database/

(see if it's actually in ~/Rosetta/main/database?)

Also consider just omitting the -database argument; Rosetta will often figure it out on its own.

Tue, 2017-11-28 13:07