Symmetry Tab

This tab provides an optional symmetry check on the input data. Symmetry of the molecule of interest represents an important piece of information about the system, and can provide additional restraint for challenging models (e.g. worse than 4.5A resolution).

When a symmetry is detected, a special Rosetta parameter file with the suffix .symm will be generated in the directory where the input file is located. The output file will be named according to the input filename e.g. if the input filename is starting_model_c7.pdb the output filename will be starting_model_c7.symm. If no symmetry is detected, no additonal settings in StarMap will be changed.

_images/symmetry_tab.png

Input file

  • Original PDB file with symmetry: Here you can select your PDB file from the file system which you want to examine. If the path and filename is longer than 60 characters, the user interface will show a shortened display name.

StarMap Symmetry check

  • Additional script options: Most commonly useful additional script options are already preset in the user interface. The options can be changed and the parameters can be set with these options:

    -r <real>

    : [default 12.0] the max CA-CA distance between two interacting chains

    -a <char>

    : [default A] the chain ID of the main chain

    -f

    : [default false] fast distance checking

  • Check: Pressing the button will execute the script in the background on the command line. If no input file was selected, the file selection dialog will appear. A short result message will be displayed in the user interface below the options line.

For the full output message the StarMap user interface opens the StarMap Log tab and displays the command line output of the execution.

_images/symmetry_log.png

If the symmetry check has been successful, the symmetry options in the Advanced tab of the user interface will be enabled, the newly generated symmetry file name will be preset and this symmetry file will be used during Shell and Rosetta execution script generation.

_images/advanced_tab_symmetry.png

The symmetry check can be used independently of the Rosetta execution and run multiple times on various data sets. For the execution scripts generation is important which symmetry values are set in the Advanced tab of the StarMap user interface.

Rosetta Symmetry check

  • Additional script options: Most commonly useful additional script options are already preset in the user interface. The following is the help output of the Rosetta commandline program make_symmdef_file.pl.

    make_symmdef_file.pl
    usage: /sw/rosetta/3.9/main/source/src/apps/public/symmetry/make_symmdef_file.pl [options]

    example: make_symmdef_file.pl -m NCS -a A -i B C -r 12.0 -p mystructure.pdb
    example: make_symmdef_file.pl -m HELIX -a A -b B -i G -r 12.0 -p mystructure.pdb
    example: make_symmdef_file.pl -m CRYST -r 12.0 -c 42.4 41.2 88.6 90.0 90.0 90.0 -s P 1 21 1 -p mystructure.pdb

    Common options:
    -m (NCS|CRYST|HELIX|PSEUDO) : [default NCS] which symmetric mode to run
    NCS: generate noncrystallographic (point) symmetries from multiple chains in a PDB file
    CRYST: generate crystallographic symmetry (fixed unit cell) from the CRYST1 line in a PDB file
    HELIX: generate helical/fiber symmetry from multiple chains in a PDB file
    PSEUDO: (EXPERIMENTAL) generate pseudo-symmetric system
    -p <string> : Input PDB file (one of -b or -p _must_ be given)
    -r <real> : [default 10.0] the max CA-CA distance between two interacting chains
    -f : [default false] enable fast distance checking (recommended for large systems)
    -q : [default false] quiet mode (no files are output)

    NCS-specific options:
    -a <char> : [default A] the chain ID of the main chain
    -d <char>* : the chain ID of other chains to keep in the output file
    -i <char>* : [default B] the chain IDs of one chain in each symmetric subcomplex
    -e : [default false] allow rigid body minimization of complete system

    CRYST-specific options:
    -c <real>x6 : override the unit cell parameters in the PDB with these values
    -g <real>x3 : perturb the unit cell parameters (A,B,C only) in the PDB with these values
    -s <string> : override the spacegroup in the PDB with these values
    -k <real> : (EXPERIMENTAL) Approximate the protein as a ball of this radius (only if no ‘-p’!)
    -h : [default false] dont restrict translational motion along axes that do not change the system

    HELIX-specific options:
    -a <char> : [default A] the chain ID of the main chain
    -b <char> : [default B] the chain ID of the next chain along the fiber/helix
    -i <char> : the chain ID of a chain in -a’s point symmetry group
    -t <real> : [default 4] the number of subunits to generate along the -b direction
    -o : [default false] make a fold-and-dock compatible symmdef file
    -e : [default false] allow rigid body minimization of complete system

    PSEUDO-specific options:
    -a <char> : [default A] the chain ID of the main chain