Expanding the silent file

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  • This topic has 2 replies, 2 voices, and was last updated 7 years ago by Anonymous.
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    • January 12, 2018 at 5:15 pm #2831
      Anonymous

        Hi Rosetta Community,

        With comparative modeling application I created a silent file output using following flags

        -out:file:silent threaded_model.out

        -out:file:silent_struct_type binary

        Later, when I used the generated silent file as an input for other applications like “cluster” or “score”, it crashed with an error.

        ERROR: Assertion `is_int( tag )` failed.

        ERROR:: Exit from: src/core/io/silent/RNA_SilentStruct.cc line: 292

         

        Is there any easy fix for that?

        Also for such silent files, is there any application to score (and output PDB) with a specific tag, for example S_XXXX_3_0258, in which I am interested?

        Thank you in advance.

         

         

      • January 15, 2018 at 3:42 am #13984
        Anonymous

          Also it appears the flag “-out:file:silent_struct_type binary”  is redundant, since the silent file with and without comes to be same. So the “new” silent file, also end up giving the same error with cluster and score applications.

          ERROR: Assertion `is_int( tag )` failed.

          ERROR:: Exit from: src/core/io/silent/RNA_SilentStruct.cc line: 292

        • January 15, 2018 at 10:35 pm #13989
          Anonymous

            For some reason, it looks like you’re reading things in as an RNA-formatted silent file, rather than a binary silent file. This is what’s leading to the errors (as there’s an apparent format mis-match) — I’m not sure why that is. You can try adding `-in:file:silent_struct_type binary` to your commandline for the programs reading your binary silent file. Normally this shouldn’t be needed, as the format of the silent struct type should be automatically determined.

            You’re correct that often times `-out:file:silent_struct_type binary` is redundant. The silent file output code will normally attempt to find the best output type, and in many cases (though not all) that’s the binary silent file format. (If you’re having issues with binary file formats, though, you may want to be explicit.)

            Regarding only working on a subset of the models, you can use the `-in:file:tags` option to list the subtags from the silent file you wish to use. This should work with any Rosetta program which reads silent files (which should be most of them).

             

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