Fit
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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 |
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>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
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