Provided by: coot_1.1.09+dfsg-2build1_amd64 
NAME
Coot - model building program for macromolecular crystallography
SYNOPSIS
coot [options]
DESCRIPTION
This manual page briefly documents the Coot molecular graphics program.
Coot is a program that displays electron density maps and models and allows certain model
manipulations: idealization, refinement, manual rotation/translation, rigid-body fitting,
ligand search, solvation, mutations, rotamers, Ramachandran plots and other stuff.
Coot has an embedded Python interpreter. Thus the full power of python is available. On
startup, Coot will look for an initialization script ($HOME/.coot.py) and will execute it
if found. This file typically contains Python commands that set personal preferences.
On exit Coot saves the current state to a file called 0-coot.state.py. This state file
contains information about the screen centre, the clipping, colour map rotation size, the
symmetry radius, and other molecule related parameters such as filename, column labels,
coordinate filename etc. The next time Coot starts up in the same directory, the user is
prompted to load the state file thus restoring the previous session.
OPTIONS
These programs follow the usual GNU command line syntax, with long options starting with
two dashes (`-'). A summary of options is included below.
--help print command line options and exit.
--detailed-help
print help, including all details and hidden options, and exit.
--full-help
print help, including hidden options, and exit.
--version
print the version and exit.
--version-full
output detailed version details and exit.
Experimental data options:
-p, --pdb <filename> ...
input PDB, SHELX .ins/.res and CIF files.
--coords, --xyzin ...
same as --pdb.
-m, --map <filename> ...
read a CCP4-format electron density map.
-d, --data, --hklin <filename> ...
MTZ, PHS or mmCIF reflection data file.
--hklin
same as --data.
-a, --auto <filename> ...
auto-read MTZ format reflection files (with default MTZ column labels FWT, PHWT).
--code <PDB ident> ...
on starting Coot, get the PDB file and MTZ file (if it exists) from the Electron
Density Server (EDS).
--dictionary <filename> ...
read in a CIF monomer dictionary.
Scripting options:
-s, --script filename ...
run a script on startup.
-c, --command command ...
run a Python command on startup.
--python
process -c arguments as Python rather than Scheme. This option only has any meaning
if Coot is built with Guile support, in which case -c arguments are considered to
be Scheme by default.
Environment:
--ccp4-project directory
optionally define CCP4 project directory.
--directory directory
Define working directory. Coot will chdir to this directory before starting any
work.
Startup options:
--no-state-script
don't run the 0-coot.state.py script on start up. Don't save a state script on exit
either.
--state-script
run the 0-coot.state.py script on start up, without popping a dialog box to prompt
the user.
--no-graphics
run Coot without graphics.
--no-guano
don't leave "Coot droppings" i.e. don't write state and history files on exit.
--no-splash-screen
don't display the pretty splash screen on startup.
--splash-screen filenameP
alternate splash screen, should be a .png format file. This option is currently
ignored.
--small-screen
start up on computer with a small screen (e.g. EEE PC and other notebook computers.
--stereo
start up in hardware stereo mode.
--side-by-side
start in side-by-side stereo mode.
--zalman-stereo
use Zalman stereo hardware.
Miscellaneous:
--host, --hostname host
start listener on host.
--port number
port number for listener define by --host.
Coot maintenance:
--update-self
attempt to update self.
--self-test
run internal self-test and exit.
EXAMPLES
For example, one might use:
coot --pdb post-refinement.pdb --auto refmac-2.mtz --dictionary lig.cif
FILES
$HOME/.coot.py
file containing user Python code, for example global personal startup settings. If
this file is found, it will be executed immediately before the state file.
$HOME/.coot-preferences/coot_preferences.py
contains global user preferences. Do not edit this file, changes will be
overwritten.
$HOME/.coot-preferences/*.py
All *.py files are loaded in alphabetical order when the program starts. The user
can place various customizations here.
./0-coot.state.py
contains the state of Coot when it last exited, for example file names of
structures and maps, the colours of the molecules and map, the screen centre, map
size and so on. When restarting a session, this file should usually be used.
./0-coot-history.py
The history of coot commands in the last coot session.
./coot-download/
Directory where the files downloaded by Coot from the network are saved. (For
example files fetched from the European Bioinformatics Institute (EBI) and the
Electron Density Server (EDS))
./coot-backup/
At each model modification a PDB file containing the current coordinates is saved
in this directory.
./coot-refmac/
When running Refmac using the Coot interface, the input and output are saved in
this directory.
./coot-ccp4/
When running CCP4 programs using the Coot interface. Input and output files are
saved in this directory.
./coot-molprobity/
When running Molprobity's Probe and Reduce using the Coot interface, the input and
output are saved in this directory.
ENVIRONMENT VARIABLES
Certain environment variables can optionally be used to modify where in the file system
Coot finds information. Default values are given in brackets.
COOT_MONOMER_LIB_DIR
Directory containing the Refmac dictionary files, used internally by Coot. This
environment variable must point to the monomers directory
[/usr/share/refmac/monomers].
COOT_REFMAC_LIB_DIR
Directory containing the Refmac dictionary files, used when Refmac or libcheck is
invoked via the Coot interface. Below the defined directory, the program must find
a data/monomers/ hierachy [/usr/share/refmac].
COOT_RESOURCES_FILE
Path to the GTK2 resource file, for customization of the widgets
[/usr/share/coot/cootrc].
COOT_SBASE_DIR
Path to the directory containing the MMDB sbase database files, that are
distributed with the CCP4 package. Coot can optionally make use of the sbase
database.
SEE ALSO
bfactan(1), density-score-by-residue(1), findligand(1), findwaters(1), fix-nomenclature-
errors(1), lidia(1).
AUTHOR
Coot is written by Paul Emsley, Kevin Cowtan, Bernhard Lohkamp, and several other
contributors.
This manual page was written for the Ubuntu coot package by Morten Kjeldgaard
<mok0@ubuntu.com>.
March 2011 COOT(1)