TriCombine

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

./modelX -f TriCombine.cfg

Or check the command line tab
Name Parameter Description Parameter Type Parameter Default
allowed-AAs List of allowed amino acids to explore string
CA-dubiety Set allowed uncertainty for CA-CA distance between triangles double 0.3
CB-dubiety Set allowed uncertainty for CB-CB distance between triangles double 1.0
combo-th Percentage of satisfaction for aminoacids for position double 1
contacts-th Number of contacts within triangles (0 means everything) int 0
context Score for context bool false
frq-only Only produce frequency matrices bool false
max-results Max number of combinations to save into results int 50000
neigh-th Distance to consider triangularization of residues double 7.5
print-trix Prints hitted triangles per position bool false
scan-residues List of residues to explore (RA124,FA122) string *
surface Only triangles involved in interactions are considered bool false
trix-table Which table of trixs you want to use string triX
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=TriCombine --CA-dubiety=0.3 --CB-dubiety=0.3 --max-threads=8 --pdb=polyA_1shg_Repair.pdb --trix-table=triX --excluded=excluded.txt --scan-residues=AA23,AA46,AA9,AA11,AA53,AA58,AA25,AA31,AA44 --combo-th=0.7 --neigh-th=7 --contacts-th=2 --allowed-AAs=AILMFWYVSTCPH --max-results=500000 --output-dir=Tricombine --database-name=PepXDB --database-server=localhost --database-user=modelx --database-pass=modelx