Bridging

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

./modelX -f Bridging.cfg

Or check the command line tab
Name Parameter Description Parameter Type Parameter Default Parameter Range
cbeta-angles Maximun allowed angle between CBs after X axis superimposition in degrees double 5 0-360
dubiety Set allowed uncertainty for the E2E dist double 0.1 0-1
mol Mol to scan with peptides string *
pep-mismatches Maximum number of mismatches for the scan peptide int 1 1;6
pepx-length Set length of the digested peptide fragments int 6 6-12
residue-begin Residue to scan with peptides int -100000
residue-begin-code Set first anchor residue code for bridging string
residue-begin-num Set first anchor residue number for bridging int NULL
residue-end Residue to scan with peptides int -100000
residue-end-code Set last anchor residue code for bridging string
residue-end-num Set last anchor residue number for bridging int NULL
sections Set circunference portions tu use as comparative rotation on X double 72 0-360
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
>modelx --command=Bridging --pdb=Bridging.pdb --pep-mismatches=2 --residue-begin=182 --residue-end=187 --mol=A --dubiety=0.1 --sections=36 --cbeta-angles=10 --database-name=ModelX --database-server=localhost --database-user=modelx --database-pass=modelx