Ok, I am running Vista and whenever I run the command line command, I press enter and there is no .pdb file. I even tried it the easy .bat file way but I cannot get that .pdb. In case I am doing something wrong here is the commands I am using..

minirosetta_2.17_windows_intelx86 -extract -all -s chk_S_00001_FastRelax__chk1_fa.out

and ...

minirosetta_2.17_windows_intelx86 -extract -all -fa_input -s chk_S_00001_FastRelax__chk1_fa.out .

What am I doing wrong? What should I do to end up with a .pdb file.

If you mean the pdb files mentioned in the How to view your structure predictions page then there is not much you can do. Unfortunately the page has not been updated in years and the instructions are only applicable to work units run using the "Rosetta Beta" code.

As far as I am aware no one has worked out how to extract the files from work units run using the newer "minirosetta" code.

I concur. The only doubt I have is if there is any dependency on type of WU. I'm not clear if the instructions don't work because the version changed, or because the type of work units changed. Since all current work seems to be using the new protocols, it is actually a moot point for the time being.

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Rosetta Moderator: Mod.Sense

Does anyone know rosetta@home's e-mail address.

You could start a note to me and I will forward as appropriate.

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Rosetta Moderator: Mod.Sense

minirosetta_2.17_windows_intelx86.exe -in:file:silent default.out -out:pdb


I love figuring these out

Actually my method doesn't work but maybe you guys could help me with the documentation at rosetta commons for input output command line...


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