CMView can be customized using key-value pairs in a
configuration file (cmview.cfg
). The example
file contains some commonly used settings. CMView is looking for
configuration files:
In the current directory
In the user's home directory
At the location specified with the command line parameter -o
If the same variable is set in more than one file, the latest value takes precedence according to the above order.
DEFAULT_CONTACT_TYPE
The contact type shown in the load dialog by default and used for graph generation when loading structures with command line parameters -p or -f
Default: Cb
DEFAULT_DISTANCE_CUTOFF
The distance cutoff shown in the load dialog by default and used for graph generation when loading structures with command line parameters -p or -f
Default: 8.0
DEFAULT_MIN_SEQSEP
The minimum sequence separation shown in the load dialog by default, negative values meaning no restraint
Default: -1
DEFAULT_MAX_SEQSEP
The maximum sequence separation shown in the load dialog by default, negative values meaning no restraint
Default: -1
CONFIG_FILE_NAME
The name of the configuration file
Default: cmview.cfg
DIST_MAP_CONTACT_TYPE
The contact type being used to calculate the distance map
Allowed values: Ca, Cb
Default: Ca
PDB_FTP_URL
A URL where PDB structures are being loaded from. (See Load from Online PDB) This can be used to load structures from a local mirrored copy of the PDB
Default: ftp\://ftp.wwpdb.org/pub/pdb/data/structures/all/mmCIF/
TEMP_DIR
The directory for storing temporary files
Default: The default system temp dir (e.g.
/tmp
or
C:\Windows\Temp
)
INITIAL_SCREEN_SIZE
The initial size in pixels of the main window on startup
Default: 650
SHOW_ICON_BAR
Whether the toolbar with command shortcut icons is shown
Default: true
SHOW_PDB_RES_NUMS
Whether legacy PDB residue numbers are shown in the lower left corner of the contact map below the secondary structure
Default: true
SHOW_RULERS
Whether secondary structure rulers are shown (above and to the left of the contact map)
Default: true
SHOW_ALIGNMENT_COORDS
Whether residue numbers in the alignment are shown in the lower left corner of the contact map (in brackets after the default residue numbers)
Default: false
USE_PYMOL
Whether PyMol specific features should be shown in the menus.
See also: PYMOL_EXECUTABLE
Default: true
USE_DSSP
Whether DSSP is used for secondary structure assigment from 3D coordinates.
See also: DSSP_EXECUTABLE
Default: true
DSSP_EXECUTABLE
The path to the local DSSP executable
DSSP_PARAMETERS
Parameters passed to DSSP when called by CMView
Default: --
PYMOL_EXECUTABLE
The path to the local PyMol executable
PYMOL_PORT
The port on which the PyMol server is listening to commands
Default: 9123
PYMOL_SHUTDOWN_ON_EXIT
Whether PyMol will be shutdown when CMView is closed
Default: true
PYMOL_LOAD_ON_START
Whether CMView will try to start PyMol on startup
Default: true
PYMOL_CONN_TIMEOUT
The time in milliseconds that CMView will wait for PyMol to startup before reporting a time out error
Default: 15000
USE_EXPERIMENTAL_FEATURES
Whether experimental features will be enabled. Experimental features are unsupported, probably not tested and are to be used on your own risk.
Default: false
SHOW_WEIGHTED_CONTACTS
Whether contacts with weights between 0 and 1 are shown as shades of grey in the contact map
Default: true
USE_DATABASE
Whether database specific features should appear in the menus
Default: true
DB_HOST
The database server for structure/graph databases
DB_PWD
The password for accessing the database
DB_USER
The username for accessing the database
DEFAULT_PDB_DB
The default database for loading structures in PDBASE format
DEFAULT_GRAPH_DB
The default database for loading contact maps
DEFAULT_MSDSD_DB
The default database for loading structures in MSDSD format