pre_bunch in new version?

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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pre_bunch in new version?

#1 Post by bear » 2020.04.18 17:55

When I try to prepare my model for bunch via pre_bunch, I do not get the normal list of questions, but:

bash-3.2$ pre_bunch
error: required argument missing SEQFILE

If I put the seq file on the command line, it next asks for FILE. I can put in one PDB file, after which it writes the output to the screen.

I would need 4 separate domains for the starting model. It used to work in the old versions like it is described in the manual.

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Usage: pre_bunch [OPTIONS] <SEQFILE> <FILE(S)>

#2 Post by AL » 2020.04.28 09:50

Indeed the manual has to be updated.
Please run pre_bunch it like this:

$pre_bunch sequence.seq domain1.pdb domain2.pdb --output my_pre_bunch.pdb

For details see:

Code: Select all

$pre_bunch --help
Usage: pre_bunch [OPTIONS] <SEQFILE> <FILE(S)>

Generates an initial approximation for further use in BUNCH

Known Arguments:
  SEQFILE                    Sequence file in FASTA format
  FILE                       Atomic coordinates in PDB or mmCIF format

Known Options:
      --center[=Y|N]         Center final structure (default: yes)
  -o, --output=<FILE>        Output filename (default: stdout)
      --seed=<INT>           Set the seed for the random number generator
  -h, --help                 Print usage information and exit
  -v, --version              Print version information and exit

Mandatory arguments to long options are mandatory for short options too.

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