Member Site › Forums › Rosetta++ › Rosetta++ – General › how do you test if your rosetta.xxx is indeed correctly built?
- This topic has 4 replies, 2 voices, and was last updated 16 years, 4 months ago by
Anonymous.
-
AuthorPosts
-
-
April 24, 2008 at 3:04 pm #549
Anonymous
beginner question…
what do you do to assess the quality of the generated executable?
(there is no “make check” or “make test”)
Is there some basic tests to run?Thanks,
Tru
-
April 28, 2008 at 1:58 pm #3934
Anonymous
If you have a rosetta.xxx successfully generated, you can run a simple test with “-s xxx.pdb -design -fixbb -natrot” to get native structure energy information
> beginner question…
>
> what do you do to assess the quality of the generated executable?
> (there is no “make check” or “make test”)
> Is there some basic tests to run?
>
> Thanks,
>
> Tru -
April 28, 2008 at 5:39 pm #3938
Anonymous
> If you have a rosetta.xxx successfully generated, you can run a simple test with “-s xxx.pdb -design -fixbb -natrot” to get native structure energy information
[tru@sillage samplerun]$ pwd
/rosetta_documentation/docking/tutorial/examples/samplerun[tru@sillage samplerun]$ ../../../../../rosetta++/rosetta.intel32-intel9-32bits.stripped -s test.pdb -design -fixbb -natrot
command executed: ../../../../../rosetta++/rosetta.intel32-intel9-32bits.stripped -s test.pdb -design -fixbb -natrot
[T/F OPT]Default FALSE value for [-no_option_display]
[T/F OPT]Default FALSE value for [-args_file]
[STR OPT]Default value for [-paths] paths.txt.
[T/F OPT]Default FALSE value for [-version]
[T/F OPT]Default FALSE value for [-score]
[T/F OPT]Default FALSE value for [-abinitio]
[T/F OPT]Default FALSE value for [-refine]
[T/F OPT]Default FALSE value for [-assemble]
[T/F OPT]Default FALSE value for [-idealize]
[T/F OPT]Default FALSE value for [-relax]
[T/F OPT]Default FALSE value for [-abrelax]
[T/F OPT]Default FALSE value for [-abrelax_mode]
[T/F OPT]New TRUE value for [-design]
[T/F OPT]Default FALSE value for [-onlypack]
[T/F OPT]New TRUE value for [-fixbb]
[T/F OPT]Default FALSE value for [-pack_in_parallel]
[T/F OPT]Default FALSE value for [-directed_design]
[REAL OPT]Default value for [-interface_electrostatic_complementarity_shift] 0
[T/F OPT]Default FALSE value for [-reverse_comp]
[INT OPT]Default value for [-conv_limit_mod] 3
[STR OPT]Default value for [-chain_in_preferred_state] none.
[STR OPT]Default value for [-chain_in_ref_state] none.
[T/F OPT]Default FALSE value for [-rotamerize]
[T/F OPT]Default FALSE value for [-point_mutation]
[T/F OPT]Default FALSE value for [-mcmin_trials]
[T/F OPT]Default FALSE value for [-output_design_movie]
[T/F OPT]Default FALSE value for [-no_new_CG]
[T/F OPT]Default FALSE value for [-multistate]
[T/F OPT]Default FALSE value for [-dna_motifs]
[REAL OPT]Default value for [-motifs_close_enough] 1.20000005
[REAL OPT]Default value for [-motifs_far_dist] 5
[REAL OPT]Default value for [-Motifs_bump_value] 100
[REAL OPT]Default value for [-motifs_match_weight] 1
[INT OPT]Default value for [-motifs_rots_required] 2
….
[REAL OPT]Default value for [-mod_hhrep_height] 1
[REAL OPT]Default value for [-mod_hhrep_width] 1
[REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
[REAL OPT]Default value for [-mod_hhrep_exponent] 4
[REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
[REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
[STR OPT]New value for [-s] test.pdb.
Starting structure: test
Reading ../../../../../rosetta_database/Rama_smooth_dyn.dat_ss_6.4
Reading ../../../../../rosetta_database/phi.theta.36.HS.resmooth
Reading ../../../../../rosetta_database/phi.theta.36.SS.resmooth
[STR OPT]Default value for [-atom_vdw_set] default.
[T/F OPT]Default FALSE value for [-IUPAC]
Atom_mode set to all
[STR OPT]Default value for [-paircutoffs] paircutoffs.
Reading ../../../../../rosetta_database/paircutoffs
[T/F OPT]Default FALSE value for [-interface_ds]
[T/F OPT]Default FALSE value for [-decoystats]
set_decoystats_flag: from,to F F
[T/F OPT]Default FALSE value for [-decoyfeatures]
[T/F OPT]Default FALSE value for [-t32s3]
[T/F OPT]Default FALSE value for [-evolution]
[T/F OPT]Default FALSE value for [-evol_recomb]
[T/F OPT]Default FALSE value for [-profile]
[T/F OPT]Default FALSE value for [-dummy_model]
[T/F OPT]Default FALSE value for [-saxs_model]
Profile defined from q = 0 to 1.
ERROR:: Can’t find starting structure: ../prepack/test.pdb
ERROR:: Exit from: input_pdb.cc line: 3028-> *** Can’t find starting structure: ../prepack/test.pdb ***
I guess I need another command to generate the “prepacked” pdbTru
-
May 5, 2008 at 1:44 pm #3941
Anonymous
It should be the path problem which specified in your path.txt. You might have the “prepacked” directory in your path file but it is not exist on your computer.
> beginner question…
>
> what do you do to assess the quality of the generated executable?
> (there is no “make check” or “make test”)
> Is there some basic tests to run?
>
> Thanks,
>
> Tru -
May 7, 2008 at 5:48 pm #3946
Anonymous
> It should be the path problem which specified in your path.txt. You might have the “prepacked” directory in your path file but it is not exist on your computer.
I completely agree to your conclusion, but **how** is the prepacked directory
generated ? I haven’t found any informations about it.Thanks
-
-
AuthorPosts
- You must be logged in to reply to this topic.