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)