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PDB file name too long to be handled by file system

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PDB file name too long to be handled by file system


in ddg_monomer module, we have encountered a problem with the length of the PDB file name when predicting mutant with 50+ mutations. Since Rosetta constructs the PDB file name based on the mutations included in the predicted mutant as prefix + list of mutations, with a large number of mutations this file name can be longer than 255 characters which causes the file system to be unable to store the PDB file. Is there any way how to prevent this behavior, for example set rosetta to store PDB file under user given name? Thank you for you answer.

Have a nice day

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Thu, 2019-08-08 03:10

One option is to store things in silent files, rather than as PDBs. You can do this by adding the option `-ddg:output_silent` to the command line, and set the filename for the silent output with the -out:file:silent option.

This will allow the ddg_monomer application to work, but you'll likely run into issues when extracting the PDBs at least if you do it in the standard fashion with the extract_pdbs application.  Luckily, though, you should be able to use a text processor (such as sed) to change the tags in the silent file from their long and unwieldy versions to a version which is easier for you to handle. You can then pass that edited file to -in:file:silent for extract_pdbs to get PDB files with filesystem friendly names.

Mon, 2019-08-26 12:17