Fit

Example Files
File Fit.pdb Binary Data Fit.cfg
Download and Copy Fit.pdb and Fit.cfg into your working directory and type:

./modelX -f Fit.cfg

Or check the command line tab
Name Parameter Description Parameter Type Parameter Default
cluster-size Set minimum cluster size int 1
extend Extend or cluster bool FALSE
pdb-1 Set pdb1 file,pdb must not be set path
pdb-2 Set pdb2 file,pdb must not be set path
rmsd-threshold Set RMSD threshold 1
Name Parameter Description Parameter Type Parameter Default Parameter Range
atom-type Atom type to be consider in the evaluation: BB,SC,ALL string BB 0-2
biassed Use biassed or non biassed forcefield bool false
command string
config Set a configuration file path
database-name Set the mySQL database name string PepXDB
database-pass Set the mySQL password string modelx
database-port Set the mySQL database port int 3306
database-server Set the mySQL server string localhost
database-user Set the mySQL username string modelx
excluded File with excluded pdb from queries path
help Show help screen
max-threads Set the maximum number of threads int 1
output-dir Set output directory path
output-file Get Pdb file without dna path noDna.pdb
pdb Set a PDB file path
pdb-dir Set PDB directory path
renumber Renumber the pdb bool false
>command=Fit --rmsd-threshold=1 --pdb-1=Fit.pdb --pdb-2=Fit.pdb --cluster-size=1 --extend=false --database-name=ModelX --database-server=localhost --database-user=modelx --database-pass=modelx