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Examples of how to run local jCE/jFatCat

The examples below will use jCE. In order to run the equivalent commands for jFatCat, use the runFatcat.sh shell script, rather than the runCE.sh

Show help

bash runCE.sh -h

Show alignment GUI

Loads the PDB files from the local file system. You might want to combine this with the -pdbDirSplit parameter, to indicate if you are using a flat installation of PDB or if it is split into sub-directories, as on the PDB-FTP web site. 
bash runCE.sh -pdb1 4hhb.A -pdb2 4hhb.B -pdbFilePath /Users/andreas/WORK/PDB/ -show3d

Automatic download of missing PDB files

The -autoFetch flag can be used to indicate that missing PDB file should be automatically downloaded and stored at the -pdbFilePath location.

Load files from a URL

This aligns the whole files, i.e. all chains. 
bash runCE.sh -file1 ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/cd/pdb1cdg.ent.gz -file2 ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/ti/pdb1tim.ent.gz -printCE

Load files from local file system

This aligns the whole file, i.e. all chains. If you want to break this up into regions, you need to manipulate the files first manually. 
bash runCE.sh -file1 /tmp/cd/pdb1cdg.ent.gz -file2  file:///tmp/ti/pdb1tim.ent.gz -printCE

Align SCOP domains

To align two SCOP domains write e.g.: 
bash runCE.sh -pdb1 d4hhba_ -pdb2 d4hhbb_ -pdbFilePath /Users/andreas/WORK/PDB/

Print internal information

Get information about the aligned fragment pairs, before they are optimized for the final alignment (CE only) 
bash runCE.sh -file1 /tmp/cd/pdb1cdg.ent.gz -file2  file:///tmp/ti/pdb1tim.ent.gz -printCE -showAFPRanges

Print output as XML

bash runCE.sh -pdb1 4hhb.A -pdb2 4hhb.B -pdbFilePath /Users/andreas/WORK/PDB/ -printXML

Write results to a file

The -outFile argument allows to write the alignment result as XML to a file. 
./runCE.sh -pdb1 d4hhba_ -pdb2 d4hhbb_ -pdbFilePath /tmp/ -outFile /tmp/tmp.out
To write the PDB files of the aligned structures, instead of the XML use the -outputPDB parameter 
./runCE.sh -pdb1 d4hhba_ -pdb2 d4hhbb_ -pdbFilePath /tmp/ -outFile /tmp/tmp.out -outputPDB

Print output in CE style

bash runCE.sh -pdb1 4hhb.A -pdb2 4hhb.B -pdbFilePath /Users/andreas/WORK/PDB/ -printCE

Print output in FatCat style

bash runCE.sh -pdb1 4hhb.A -pdb2 4hhb.B -pdbFilePath /Users/andreas/WORK/PDB/ -printFatCat

Run a DB search

bash runCE.sh -pdbFilePath /Users/ap3/WORK/PDB/ -alignPairs ./example.lst -outFile db.out
The DB search requires an inputfile (here: example.lst). In this file a line has to contain two protein pairs to align. Example: 
# an example input for a DB search
				4hhb.C 4hhb.D
				4hhb:0 4hhb:1
				1cdg.A 1tim.B
				1hiv.A 1a4w.H
				1RLW 1BYN
				2sim 1nsb
				1CEW 1mol
				1TEN 3HHR
				4hhb:(A:10-40,B:10-40) 4hhb:(C:10-40,D:10-40)

How to specify protein pairs:
PDB codes are case insensitive.
Definition of separators: The character "." splits PDB codes and chain IDs. If the separator ":" is used, the code assumes that chains are accessed by their position. 0 refers to the first chain in the structure.
Chain IDs are case sensitive. If a lower case chain ID is provides, which is not found in the PDB file, the code attempts to convert the chain ID to upper case.
If no chain ID is provides, the code tries to align the whole set of atoms in a PDB file. (note: this can be slow).

View DB search results

bash runCE.sh -pdbFilePath /Users/ap3/WORK/PDB/ -viewDBresult db.out

Legacy CE source code

A copy of the old CE source code is still available from here.