Command: log

Usage:
log [ thumbnail [ width w ][ height h ]] [ text | html  character string ]

Usage:
log ( show | hide | clear )

Usage:
log settings [ errorDialog  true | false ] [ warningDialog  true | false ]

The log command acts on the Log. See also: Log preferences, Command History, ChimeraX browser, usage, measurements

Options of the main log command add images and/or specified text:

• thumbnail - include a thumbnail image of the current display; pixel width and height can be specified (default 100 x 100)
• text - echo the rest of the command (up to the next carriage return or semicolon, including any spaces) in the Log; must be the last option in the command
• html - render the rest of the command (up to the next carriage return or semicolon, including any spaces) as HTML in the Log; must be the last option in the command, for example:

  log thumb html <b>Toxin from <i>Bacillus thuringiensis</i></b>

Subcommands:

• log show – open the Log
• log hide – close the Log
• log clear – clear the contents
• log settings – whether errors/warnings should raise dialogs (in the current session; can be saved for later sessions in the Log preferences)
• log save – save contents to an HTML file
• log metadata – show metadata associated with a model (literature citation, etc.)
• log chains – show an interactive table of the biopolymer chains in a model

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Saving to HTML

Usage: log save  pathname  [ executableLinks  true | false ]

The log save command saves the contents of the Log as an HTML file of specified pathname (or the word browse to specify it interactively in a file browser window). The executableLinks option specifies whether the command links in the file should be executable (when the file is viewed with the ChimeraX browser) or go to command help pages. If link type is not specified, the file will contain the same type of links as in the current Log, which can be set with its context menu.

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Model Information

Usage: log metadata  model-spec  [ verbose  true | false ]
Usage: log chains  model-spec 

The subcommand log metadata reports model metadata in the Log. Metadata is associated information read from the input file, such as literature citation, experimental method, resolution, and associated cryo-electron microscopy map (Electron Microscopy Data Bank entry), if applicable. Using verbose true shows all available information, sometimes the same as with verbose false (depending on what is available). Currently, metadata is read from the mmCIF and PDB input formats.

The subcommand log chains shows a table of the model's biopolymer chains, in which:

• clicking a chain identifier selects the corresponding chain in the structure
• clicking a chain description opens the sequence in the Sequence Viewer, associated with all of the corresponding chains in the structure
• clicking a UniProt identifier fetches the corresponding protein sequence and its sequence feature annotations, and clicking the residue number range (with numbering according to the structure) selects the corresponding structure residues; multiple UniProt identifiers and residue ranges may be given for a fusion protein

See also: info, Model Panel buttons, model information