SPARTAN08_Fixer is a program that fixes single chain Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol.
- Available in webserver form so no installation needed, unless you have A LOT of files to convert
- command line version allows single files or entire folders of PDB files to be converted automagically.
- conforms to PDB format specifications as described here and here
- At the above site, you can find a server where you can paste in a file and have it processed by the SPARTAN08_Fixer program.
- If you have a lot of files to convert or need greater customization in your workflow than you'll want the command line version SPARTAN08_Fixer_standalone.py downloadable in this repository.
The command line version, called SPARTAN08_Fixer_standalone.py, downloadable here in this repository.
MANUAL/HELP OPTION for command line version
python SPARTAN08_Fixer.py --help
usage: SPARTAN08_Fixer.py [-h] [--ChainDesig X] [--StartNo Y] [-a] InputData SPARTAN08_Fixer is a program that fixes single chain Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol. Written by Wayne Decatur --> Fomightez @ Github or Twitter. PDB format specification info: http://www.wwpdb.org/docs.html and http://deposit.rcsb.org/adit/docs/pdb_atom_format.html Actual example what to enter on command line to run program: python SPARTAN_FIXER input_file.pdb positional arguments: InputData name of Spartan data file that will be fixed. REQUIRED. Files entered this way do not have any requirement for specific extension as long they are SPARTAN so-called PDB formatted-data. The required input data can also be a group of files ending in '.pdb' (case does not matter) contained within a folder. In that case put the folder as the input data. optional arguments: -h, --help show this help message and exit --ChainDesig X Enter in place of 'X' an alphanumeric character to use as chain designation, or enter when prompted --StartNo Y Enter in place of 'Y' a number in the range 1 to 9999 to be the first residue sequence number for the output, or enter when prompted -a, --auto Run without further prompts for user action, using chain designation and starting residue on command line or the defaults of 'A' and '1', respectively, for those values if none provided.
Typical examples of use of command line version
python SPARTAN08_Fixer.py spartanPDBfile.pdb
You'll be prompted to enter chain identifier designation and a number at which to start the residue numbering.
Typical run, specifying the options at the command line
python SPARTAN08_Fixer.py spartanPDB.pdb --ChainDesig G --StartNo 7
Running on PDB files in a directory
python SPARTAN08_Fixer.py TheDirectory
Running on PDB files in a directory with default settings without prompts
python SPARTAN08_Fixer.py TheDirectory --auto
Running on PDB files in a directory using command line to designate values
python SPARTAN08_Fixer.py TheDirectory --ChainDesig Z --StartNo 16