GodzikLab / FATCAT-dist

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FATCAT package

(Flexible structural AlignmenT by Chaining AFPs with Twist)

Intro

FATCAT is the software package behind https://fatcat.godziklab.org

Installation

Run

./Install

If Install fails, please go to the FATCATMain directory and modify the basic.h file that includes all the head files. Then run

make


FATCAT usages

Program 1: FATCAT (main program)

note: all the output pdb files include two chains with chain A for pdb 1 and chain B for pdb 2


Program 2: FATCATQue.pl

purpose: a script for runing FATCAT on a list of structure pairs

command: FATCATQue.pl log-file pair-list-file


Program 3: FATCATSearch.pl

purpose: a script for runing FATCAT for a query against a database command: FATCATQue.pl query target-list parameters.. note: for this purpose, you need to prepare a database of protein structures


FATCAT Tests

1. FATCAT for a single pair of structures

Go to ./Examples_FATCAT,

run FATCAT for structure 1a21A.pdb and 1hwgC.pdb

command: FATCAT -p1 1a21A.pdb -p2 1hwgC.pdb -o 1a21A_1hwgC -m -ac -t

inputs: 
  structure 1a21A.pdb and 1hwgC.pdb

outputs: (a twist is detected in comparing these two structures)

  1a21A_1hwgC.aln               # alignment result between the two structures
  1a21A_1hwgC.afp.color.ps      # the AFP chaining result of the FATCAT in postscript graph
  1a21A_1hwgC.opt.twist.pdb     # the pdb file in which 1a21A.pdb in chain A, twisted 1hwgC.pdb in chain B  
                                # refer REMARK lines in the begining of .pdb file
  1a21A_1hwgC.opt.twist.script  # the rasmol script for viewing 1a21A_1hwgC.opt.twist.pdb 
                                # blocks of 1hwgC.pdb are shown in different colors
                                # command: rasmol -script 1a21A_1hwgC.opt.twist.script

Please compare 1a21A_1hwgC.aln with compare.aln file. If no difference is found between these two files, FATCAT runs ok.

2. FATCAT for a list of pairs

Go to ./Examples2_FATCAT

command:
 ../FATCATMain/FATCATQue.pl timeused allpair.list -q >allpair.aln
(note: this calculation takes about 30 min on Intel(R) XEON(TM) CPU 1.80GHz)

input: allpair.list (the list of pairs) and the corresponding pdb files
output: allpair.aln (the text file of all the alignments)

Please compare allpair.aln with allpair.aln.comp. If no difference is found, FATCAT runs ok.

for testing a smaller set of pairs:

command:
../FATCATMain/FATCATQue.pl timeused prtpair.list -q >prtpair.aln

(note: this calculation takes about 10 min on Intel(R) XEON(TM) CPU 1.80GHz)