Configuration

Overview

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:

  1. In the current directory

  2. In the user's home directory

  3. 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.

Available configuration parameters:

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

Parameters affecting experimental features:

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