Call scancel to cancel a consecutive set of cluster job numbers

usage: [-h]

Converts images to TIFF figures at 300 DPI for publication using sips. Arguments: INFILE OUTFILE

usage: [-h]

This script outputs fasta files from a genscript format. Pass the –format option to control which genscript format as input ~~~ Ex: python –format mutagenesis MutagenesisFormatU68 ~~~

usage: [-h] --format {mutagenesis,GeneSynth} infile

Positional Arguments

infile The mutagenesis format file.

Named Arguments


Possible choices: mutagenesis, GeneSynth

The genscript file format

Uses Biopython to print sequence information. Example: –pdb 2j88_A.pdb –format fasta –outpath test.txt

usage: [-h] [--pdb PDB] [--pdblist PDBLIST]
                  [--pdblist_input_dir PDBLIST_INPUT_DIR] [--chain CHAIN]
                  [--cdr CDR]
                  [--format {basic,fasta,general_order,IgG_order,IgG_order_lambda,IgG_order_kappa,IgG_order_heavy}]
                  [--outpath OUTPATH] [--prefix PREFIX] [--region REGION]
                  [--strip_c_term STRIP_C_TERM] [--pad_c_term PAD_C_TERM]

Named Arguments

--pdb, -s Input PDB path
--pdblist, -l Input PDB List
--pdblist_input_dir, -i
 Input directory if needed for PDB list
--chain, -c

A specific chain to output

Default: “”


Pass a specific CDR to output alignments of.

Default: “”


Possible choices: basic, fasta, general_order, IgG_order, IgG_order_lambda, IgG_order_kappa, IgG_order_heavy

The output format requried.

Default: “fasta”

--outpath, -o Output path. If none is specified it will write to screen.
--prefix, -t

Tag to add before chain

Default: “”

--region specify a particular region, start:end:chain
--strip_c_term Strip this sequence off the C-term of resulting sequences. (Useful for antibodies
--pad_c_term Pad this sequence with some C-term (Useful for antibodies

Output the original sequence and the striped seqeunce if stripped. Default FALSE.

Default: False

Renames original files to new names for design ordering. Copy all models going to be ordered into a single directory first. Run from directory with pdb files already copied in!

usage: [-h] -i NEW_NAMES

Named Arguments

-i, --new_names
 File with new to old names. Example line: new_name * filename. Can have lines that don’t have all three. Will only rename if it has a star in the second column.