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
[back to top: log]
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.
[back to top: log]
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
UCSF Resource for Biocomputing, Visualization, and Informatics /
August 2023