It has been painfully hard to find a way to view my predictions in PDB format by running a command line to convert a silent file to a pdb file on Windows.... This is very useful because PyMol can help view the alignment of my prediction to the native structure.... Yes, there is a page on how to view structure predictions, but the -extract command is no longer implemented.... There must be some other way, and I have been looking through the Rosetta Commons documentation but haven't found one yet....


PLEASE HELP ME WITH THIS!!

This has been long unsolved


-Michael D.

I'll update the instructions. It may be different with the various jobs using different protocols etc...

How long is it expected to take

I'll update the instructions. It may be different with the various jobs using different protocols etc...

How long will it take

I can look into it Tuesday. It shouldn't take that long but it likely will not work for all workunits.

If you're an academic you can get a rosetta license, build the package, and use the score application for extracting pdbs.

http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_scoring.html

I can look into it Tuesday. It shouldn't take that long but it likely will not work for all workunits.

If you're an academic you can get a rosetta license, build the package, and use the score application for extracting pdbs.

http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_scoring.html

Are you going to update it tonight then

I'm having to build a special extractor binary for all three platforms. Still building the mac platform, the linux one finished, and I have to start working on the windows one which will take some time. I'll be lucky to have it done today unfortunately but will keep working on it.

did you try extracting with the old rosetta++ binary?

depending on your platform:

https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_i686-apple-darwin
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_i686-pc-linux-gnu
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_powerpc-apple-darwin
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_windows_intelx86.exe
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_windows_x86_64.exe
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_x86_64-pc-linux-gnu


The current instructions are based on this application but will not work for some result formats.

did you try extracting with the old rosetta++ binary?

depending on your platform:

https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_i686-apple-darwin
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_i686-pc-linux-gnu
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_powerpc-apple-darwin
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_windows_intelx86.exe
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_windows_x86_64.exe
https://boinc.bakerlab.org/rosetta/download/rosetta_5.82_x86_64-pc-linux-gnu


The current instructions are based on this application but will not work for some result formats.

Yes I did, this was mentioned in previous threads, but this won't work.... Something about Rama_smooth_dyn.dat_ss_6.4


It would be very helpful to post new instructions.

Instructions will not help without the new binaries that I'm currently building. There's no other way to extract decoys now unless you have the old rosetta application and the old database around but even with that, it will not guarantee being able to extract the different work unit dependent formats.

Still trying to build the windows platform but I'm having trouble accessing our network now from home.

I wasn't able to get the windows build to work. It will take some more time. You'll have to wait a few days because I have jury duty starting tomorrow. Sorry, but it's not trivial and requires a bit of work.

If you have access to a mac or linux platform, you can get the extract_pdbs binaries at:

https://boinc.bakerlab.org/rosetta/rah_misc/extractor/

you can run with -help to get command line options.

basically you'll have to run a command like:

extract_pdbs.macosgccrelease -in:file:silent default.out -database minirosetta_database in the slot directory that contains your result file and minirosetta_database.

I'll post detailed instructions once I have the windows platform up.

I wasn't able to get the windows build to work. It will take some more time. You'll have to wait a few days because I have jury duty starting tomorrow. Sorry, but it's not trivial and requires a bit of work.

If you have access to a mac or linux platform, you can get the extract_pdbs binaries at:

https://boinc.bakerlab.org/rosetta/rah_misc/extractor/

you can run with -help to get command line options.

basically you'll have to run a command like:

extract_pdbs.macosgccrelease -in:file:silent default.out -database minirosetta_database in the slot directory that contains your result file and minirosetta_database.

I'll post detailed instructions once I have the windows platform up.

Yeh thanks David

Let me know how the mac and linux extract_pdbs app works for you all.

Still trying to build the windows version.

Okay, I was able to build the windows version and it is now available at:

https://boinc.bakerlab.org/rosetta/rah_misc/extractor/

extract_pdbs.exe

I'll update the instructions soon. Basically, if you have cygwin installed or are familiar with the command prompt, you can use the following command in a terminal:

./extract_pdbs.exe -in:file:silent default.out -database minirosetta_database

in the slot directory that has default.out and minirosetta_database.

It should extract into PDB files named S_00000001.pdb, etc.

or you can create a ".bat" batch file containing the command above and execute it as described windows section in the instructions for the older rosetta app (https://boinc.bakerlab.org/rosetta/rah_view_predictions.php).

More information about the extract_pdbs application is available at:

http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_silentfile.html

.extract_pdbs.exe -in:file:silent default.out -database minirosetta_database -in::file::silent_struct_type 'protein'

isn't working

.extract_pdbs.exe -in:file:silent default.out -database minirosetta_database -in::file::silent_struct_type 'protein'

isn't working

I need more info. What's being printed out to the terminal? Which work unit is it?

The first thing is I am getting a pdb file using your normal script that is all right except for an inexplicable entity in the center of it (I call it protein garbage, you may call it as you wish :) )

The second thing is the command line I posted many hours ago which technically should extract results from pdb silent file structs rather than binaries. But it is not working.

The next time I have a rosetta work unit.... Probably tomorrow.... I will post the command line output.... but it should probably not be necessary because the protein garbage will probably happen on any computer running windows that runs the conversion program

.extract_pdbs.exe -in:file:silent default.out -database minirosetta_database -in::file::silent_struct_type 'protein'

isn't working

I need more info. What's being printed out to the terminal? Which work unit is it?

e/trunk/mini
core.init: command: extract_pdbs.exe -in:file:silent chk_S_00013_FragmentSampler
__rg_state.out -database minirosetta_database
core.init: 'RNG device' seed mode, using 'CryptGenRandom', seed=-1820135110 seed
_offset=0 real_seed=-1820135110
core.init.random: RandomGenerator:init: Normal mode, seed=-1820135110 RG_type=mt
19937
Warning: Unable to locate database file chemical/atom_type_sets/fa_standard/
core.io.silent: Reading all structures from chk_S_00013_FragmentSampler__rg_stat
e.out
core.io.silent: Finished reading 1 structures from chk_S_00013_FragmentSampler__
rg_state.out
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy w
ell
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis
= 6)
core.scoring.etable: Finished calculating energy tables.
core.io.database: Database file opened: minirosetta_databasepdb_pair_stats_fine

core.io.database: Database file opened: minirosetta_databasescoring/score_funct
ions/hbonds/standard_params/HBPoly1D.csv
core.io.database: Database file opened: minirosetta_databasescoring/score_funct
ions/hbonds/standard_params/HBFadeIntervals.csv
core.io.database: Database file opened: minirosetta_databasescoring/score_funct
ions/hbonds/standard_params/HBEval.csv
core.io.database: Database file opened: minirosetta_databaseP_AA.gz
core.io.database: Database file opened: minirosetta_databaseP_AA_n.gz
core.io.database: Database file opened: minirosetta_databaseP_AA_pp.gz
core.io.database: Database file opened: minirosetta_databaseRama_smooth_dyn.dat
_ss_6.4.gz
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 1 natoms_pose=14atm_seqpos 1 natoms
_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 2 natoms_pose=11atm_seqpos 2 natoms
_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 3 natoms_pose=22atm_seqpos 3 natoms
_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 4 natoms_pose=19atm_seqpos 4 natoms
_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 5 natoms_pose=11atm_seqpos 5 natoms
_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 6 natoms_pose=21atm_seqpos 6 natoms
_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 7 natoms_pose=19atm_seqpos 7 natoms
_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 8 natoms_pose=19atm_seqpos 8 natoms
_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 9 natoms_pose=12atm_seqpos 9 natoms
_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 10 natoms_pose=7atm_seqpos 10 natom
s_struct=6)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 11 natoms_pose=19atm_seqpos 11 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 12 natoms_pose=19atm_seqpos 12 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 13 natoms_pose=20atm_seqpos 13 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 14 natoms_pose=19atm_seqpos 14 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 15 natoms_pose=21atm_seqpos 15 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 16 natoms_pose=7atm_seqpos 16 natom
s_struct=6)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 17 natoms_pose=16atm_seqpos 17 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 18 natoms_pose=19atm_seqpos 18 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 19 natoms_pose=19atm_seqpos 19 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 20 natoms_pose=14atm_seqpos 20 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 21 natoms_pose=10atm_seqpos 21 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 22 natoms_pose=19atm_seqpos 22 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 23 natoms_pose=20atm_seqpos 23 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 24 natoms_pose=19atm_seqpos 24 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 25 natoms_pose=24atm_seqpos 25 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 26 natoms_pose=16atm_seqpos 26 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 27 natoms_pose=22atm_seqpos 27 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 28 natoms_pose=20atm_seqpos 28 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 29 natoms_pose=11atm_seqpos 29 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 30 natoms_pose=24atm_seqpos 30 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 31 natoms_pose=11atm_seqpos 31 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 32 natoms_pose=10atm_seqpos 32 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 33 natoms_pose=13atm_seqpos 33 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 34 natoms_pose=14atm_seqpos 1 natom
s_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 35 natoms_pose=11atm_seqpos 2 natom
s_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 36 natoms_pose=22atm_seqpos 3 natom
s_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 37 natoms_pose=19atm_seqpos 4 natom
s_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 38 natoms_pose=11atm_seqpos 5 natom
s_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 39 natoms_pose=21atm_seqpos 6 natom
s_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 40 natoms_pose=19atm_seqpos 7 natom
s_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 41 natoms_pose=19atm_seqpos 8 natom
s_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 42 natoms_pose=12atm_seqpos 9 natom
s_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 43 natoms_pose=7atm_seqpos 10 natom
s_struct=6)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 44 natoms_pose=19atm_seqpos 11 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 45 natoms_pose=19atm_seqpos 12 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 46 natoms_pose=20atm_seqpos 13 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 47 natoms_pose=19atm_seqpos 14 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 48 natoms_pose=21atm_seqpos 15 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 49 natoms_pose=7atm_seqpos 16 natom
s_struct=6)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 50 natoms_pose=16atm_seqpos 17 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 51 natoms_pose=19atm_seqpos 18 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 52 natoms_pose=19atm_seqpos 19 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 53 natoms_pose=14atm_seqpos 20 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 54 natoms_pose=10atm_seqpos 21 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 55 natoms_pose=19atm_seqpos 22 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 56 natoms_pose=20atm_seqpos 23 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 57 natoms_pose=19atm_seqpos 24 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 58 natoms_pose=24atm_seqpos 25 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 59 natoms_pose=16atm_seqpos 26 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 60 natoms_pose=22atm_seqpos 27 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 61 natoms_pose=20atm_seqpos 28 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 62 natoms_pose=11atm_seqpos 29 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 63 natoms_pose=24atm_seqpos 30 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 64 natoms_pose=11atm_seqpos 31 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 65 natoms_pose=10atm_seqpos 32 nato
ms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At
tempting to continue ...
core.io.silent: [ WARNING ] (in residue 66 natoms_pose=13atm_seqpos 33 nato
ms_struct=7)

extract_pdbs.
exe -in:file:silent default.out -database minirosetta_database
core.init: Mini-Rosetta version 34709M from https://svn.rosettacommons.org/sourc
e/trunk/mini
core.init: command: extract_pdbs.exe -in:file:silent default.out -database minir
osetta_database
core.init: 'RNG device' seed mode, using 'CryptGenRandom', seed=96414181 seed_of
fset=0 real_seed=96414181
core.init.random: RandomGenerator:init: Normal mode, seed=96414181 RG_type=mt199
37
Warning: Unable to locate database file chemical/atom_type_sets/fa_standard/

ERROR: ERROR: Unable to open silent_input file: 'default.out'
ERROR:: Exit from: ....srccoreiosilentSilentFileData.cc line: 86

extract_pdbs.
exe -in:file:silent default.out -database minirosetta_database
core.init: Mini-Rosetta version 34709M from https://svn.rosettacommons.org/sourc
e/trunk/mini
core.init: command: extract_pdbs.exe -in:file:silent default.out -database minir
osetta_database
core.init: 'RNG device' seed mode, using 'CryptGenRandom', seed=96414181 seed_of
fset=0 real_seed=96414181
core.init.random: RandomGenerator:init: Normal mode, seed=96414181 RG_type=mt199
37
Warning: Unable to locate database file chemical/atom_type_sets/fa_standard/

ERROR: ERROR: Unable to open silent_input file: 'default.out'
ERROR:: Exit from: ....srccoreiosilentSilentFileData.cc line: 86

You need to run it in the same directory where default.out and minirosetta_database exists. It's not finding these. I'm not sure what's happening with your other post. May be an incompatible silent mode format which you will not be able to extract. I need the work unit names to look into these issues further.

Not all results will be able to be extracted. Please keep this in mind.