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.

You can see the problem much better if you view the structure in a molecular viewing program as wireframe

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.

mem_widd_run03_centroid 2rlf and 2k73 PBID's

okay now here is an image of what it looks like when I am viewing my outputted structure prediction

http://img199.imageshack.us/i/33216778.png/

okay now here is an image of what it looks like when I am viewing my outputted structure prediction

http://img199.imageshack.us/i/33216778.png/

Do you see the problem now?

If I may comment again on this age-old thread... The extract_pdbs.bat is not working again... But may I request kindly that Rosetta@home makes a utility to extract all types of files into their PDB predictions from silent file format

Where's support... Do they read these messages... It's been 10 days... FEEDBACK please. There must be a command line switch since the Rosetta staff obviously can convert the files using Rosetta

The extract_pdbs.bat is not working again...

Hi Mike, sorry for the delay in getting back to you. Unfortunately, due to the diversity of protocols that are being used currently, we aren't supporting extract_pdbs.bat anymore. (We use other methods to extract/look at the results, ones that aren't straightforward to replicate on the client computers.)

In the future we might resume support for extracting and examining structures from Rosetta@home workunits, but the people who would handle that are very busy with other projects, and it's low on the priority list.