Documentation Command Line Arguments

Documentation of jCE and jFATCAT command line options.

-h, -help, --help Show help on command line

User Interface

-showMenu displays the menu that allows to run alignments through a user interface.

Pairwise alignments

There are two main ways how to specify what to align. One way is to specify exact file names using the -file1/-file2 options. The second approach uses the naming convention specified below for describing what to align. It uses the -pdb1/-pdb2 and -pdbFilePath options.

Specifying file names

-file1 -file2 specifies two files to be aligned. Uses the full content of the files for alignment.

Specifying names

-pdb1 -pdb2 specifies two names for alignment. See Naming convention below for supported names.

-pdbFilePath specifies a path in the local file system which contains a local copy of PDB files.

-autoFetch(optional) automatically download missing PDB entries and store them in -pdbFilePath . If set to true PDB files will automatically get downloaded. (default: false)

-pdbDirSplit(optional) Define if the directory containing PDB files has all PDBs in one level or is split into multiple subdirs, like the ftp site. (default and recommended: true)

Naming convention

The -pdb1 and -pdb2 arguments allow to request the alignment of a name which describes what should be aligned. Formal specification for how to specify the name:
		name     := pdbID
		               | pdbID '.' chainID
		               | pdbID '.' range
		               | scopID
		range         := '('? range (',' range)? ')'?
		               | chainID
		               | chainID '_' resNum '-' resNum
		pdbID         := [0-9][a-zA-Z0-9]{3}
		chainID       := [a-zA-Z0-9]
		scopID        := 'd' pdbID [a-z_][0-9_]
		resNum        := [-+]?[0-9]+[A-Za-z]?

		Example structures:
		1TIM     #whole structure
		4HHB.C     #single chain
		4GCR.A_1-83     #one domain, by residue number
		3AA0.A,B     #two chains treated as one structure
		d2bq6a1     #scop domain

Working with custom and non-public files

jCE and jFATCAT support alignment of files that are not in PDB. The alignment can be specified either by providing the path to the file using the -file1 and -file2 options or by providing URLs that describe where to find the files for the -pdb1 and -pdb2 options.

Here's how to specify a relative path to files:
bash -file1 ./tmp/mytest1.pdb -file2 ./tmp/mytest2.pdb -show3d
And here how to use URLs
bash -pdb1 file:///Users/andreas/Downloads/mytest1.pdb -pdb2 file:///Users/andreas/Downloads/mytest2.pdb -show3d
This feature also allows to fetch files on the fly from a remote site:
bash -file1 -file2 -show3d
bash -pdb1 -pdb2 -show3d

Output options

There are a number of different types of output

-show3d Show a graphical user interface that allows a detailed analysis of the output. For example the following command line gives the screenshot shown below:
bash -pdb1 4hhb.A -pdb2 4hhb.B -pdbFilePath /tmp/ -autoFetch -show3d

More output options

-printXML true/false print the XML representation of the alignment on stdout.

-printFatCat true/false print the original FATCAT output to stdout.

-printCE true/false print the result in CE style

-outFile file to write the output to (default: writes XML representation).

-outputPDB use this flag together with -outFile to dump the PDB file of the aligned structures, instead of the XML representation, instead of XML

Database searches

-alignPairs path to a file that contains a set of pairs to compare. The included example.lst file demonstrates how this can be used.

-searchFile path to a PDB file that should be used in a Database Search.

-outFile (mandatory) a directory that will contain the summary of all the pairwise alignments

-pdbFilePath (mandatory) Path to the directory in your file system that contains the PDB files.

-saveOutputDir (optional) a directory that will contain the detailed outputs of the alignments. By default will write XML files, if used together with -outputPDB, will write PDB files of the alignment.

-nrCPU (optional) Number of CPUs to use for the database search. By default will use the all, but one CPU in the system.

Once DB seaches are complete it is possible to view the results with:

-showDBresult (optional) path to a DB outFile to show. Also provide the -pdbFilePath parameter to enable visualisation of results.

jCE specific options

-maxGapSize (optional, jCE specific): set the maximum gap size parameter G during AFP extension. default: 30. Set to 0 for unrestricted.

-showAFPRanges (optional, jCE specific): show the raw Aligned Fragment Pair positions, prior to optimization.

jFATCAT specific options

-flexible (optional, jFATCAT specific): true/false, defines if the alignment should be run in flexible or rigid mode. The default is to run alignments in rigid mode (-flexible false)