# Expanding the silent file

3 posts / 0 new
Expanding the silent file
#1

Hi Rosetta Community,

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

-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?

Post Situation:
Fri, 2018-01-12 09:15
jharamesh

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

Sun, 2018-01-14 19:42
jharamesh

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).

Mon, 2018-01-15 14:35
rmoretti