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Reference


accept

SECURITY FEATURE


alias

DESCRIPTION

   "alias" allows you to bind a commonly used command to a single PyMOL keyword.

USAGE

   alias name, command-sequence

PYMOL API

   cmd.alias(string name,string command)

EXAMPLES

   alias go,load $TUT/1hpv.pdb; zoom 200/; show sticks, 200/ around 8
   go

NOTES

   For security reasons, new PyMOL commands created using "extend" are
   not saved or restored in sessions.

SEE ALSO

   extend, api


align

DESCRIPTION

   "align" performs a sequence alignment followed by a structural
   alignment, and then carrys out zero or more cycles of refinement
   in order to reject structural outliers found during the fit.

USAGE 

   align (source), (target) [,cutoff [,cycles [,gap [,extend \
         [,skip [,object [,matrix [, quiet ]]]]]]]]

PYMOL API

   cmd.align( string source, string target, float cutoff=2.0,
              int cycles=2, float gap=-10.0, float extend=-0.5,
              float extend=-0.5,int skip=0, string object=None,
              string matrix="BLOSUM62",int quiet=1 )

NOTE

   If object is not None, then align will create an object which
   indicates which atoms were paired between the two structures

EXAMPLES

   align  prot1////CA, prot2, object=alignment

SEE ALSO

   fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit


alt_special

dict() -> new empty dictionary.
dict(mapping) -> new dictionary initialized from a mapping object's
    (key, value) pairs.
dict(seq) -> new dictionary initialized as if via:
    d = {}
    for k, v in seq:
        d[k] = v


alter

DESCRIPTION

   "alter" changes one or more atomic properties over a selection
   using the python evaluator with a separate name space for each
   atom.  The symbols defined in the name space are:

      name, resn, resi, chain, alt, elem, q, b, segi,
      type (ATOM,HETATM), partial_charge, formal_charge,
      text_type, numeric_type, ID

   All strings must be explicitly quoted.  This operation typically
   takes several seconds per thousand atoms altered.

   WARNING: You should always issue a "sort" command on an object
   after modifying any property which might affect canonical atom
   ordering (names, chains, etc.).  Failure to do so will confound
   subsequent "create" and "byres" operations.

USAGE

   alter (selection),expression

EXAMPLES

   alter (chain A),chain='B'
   alter (all),resi=str(int(resi)+100)
   sort

SEE ALSO

   alter_state, iterate, iterate_state, sort


alter_state

DESCRIPTION

   "alter_state" changes the atomic coordinates of a particular state
   using the python evaluator with a separate name space for each
   atom.  The symbols defined in the name space are:

      x,y,z

USAGE

   alter_state state,(selection),expression

EXAMPLES

   alter_state 1,(all),x=x+5

SEE ALSO

   iterate_state, alter, iterate


attach

DESCRIPTION

   "attach" adds a single atom onto the picked atom.

USAGE

   attach element, geometry, valence

PYMOL API

   cmd.attach( element, geometry, valence )

NOTES

   Immature functionality.  See code for details.


backward

DESCRIPTION

   "backward" moves the movie back one frame.

USAGE

   backward

PYMOL API

   cmd.backward()

SEE ALSO

   mset, forward, rewind


bg_color

DESCRIPTION

   "bg_color" sets the background color

USAGE

   bg_color [color]

PYMOL API

   cmd.bg_color(string color="black")


bond

DESCRIPTION

   "bond" creates a new bond between two selections, each of
   which should contain one atom.

USAGE

   bond [atom1, atom2 [,order]]

PYMOL API

   cmd.bond(string atom1, string atom2)

NOTES

   The atoms must both be within the same object.

   The default behavior is to create a bond between the (lb) and (rb)
   selections.

SEE ALSO

   unbond, fuse, attach, replace, remove_picked


button

DESCRIPTION

   "button" can be used to redefine what the mouse buttons do.

USAGE

   button <button>,<modifier>,<action>

PYMOL API

   cmd.button( string button, string modifier, string action )

NOTES

   button:      L, M, R, S
   modifers:    None, Shft, Ctrl, CtSh
   actions:     Rota, Move, MovZ, Clip, RotZ, ClpN, ClpF
                lb,   mb,   rb,   +lb,  +lbX, -lbX, +mb,  +rb, 
                PkAt, PkBd, RotF, TorF, MovF, Orig, Cent


cartoon

DESCRIPTION

   "cartoon" changes the default cartoon for a set of atoms.

USAGE

   cartoon type, (selection)

   type = skip | automatic | loop | rectangle | oval | tube | arrow | dumbbell

PYMOL API

   cmd.cartoon(string type, string selection )

EXAMPLES

   cartoon rectangle,(chain A)
   cartoon skip,(resi 145:156)

NOTES

   the "automatic" mode utilizes ribbons according to the
   information in the PDB HELIX and SHEET records.


cd

DESCRIPTION

   "cd" changes the current working directory.

USAGE

   cd <path>

SEE ALSO

   pwd, ls, system


center

DESCRIPTION

   "center" translates the window, the clipping slab, and the
   origin to a point centered within the atom selection.

USAGE

   center [ selection [,state [, origin]]]

EXAMPLES

   center 145/

PYMOL API

   cmd.center( string selection, int state = 0, int origin = 1 )

NOTES

   state = 0 (default) use all coordinate states
   state = -1 use only coordinates for the current state
   state > 0  use coordinates for a specific state

   origin = 1 (default) move the origin
   origin = 0 leave the origin unchanged

SEE ALSO

   origin, orient, zoom


clip

DESCRIPTION

   "clip" alters the near and far clipping planes

USAGE

   clip {near|far|move|slab|atoms}, distance [,selection [,state ]]

EXAMPLES

   clip near, -5           # moves near plane away from you by 5 A
   clip far, 10            # moves far plane towards you by 10 A
   clip move, -5           # moves the slab away from you by 5 A
   clip slab, 20           # sets slab thickness to 20 A
   clip slab, 10, resi 11  # clip 10 A slab about residue 11

   clip atoms, 5, pept     # clip atoms in "pept" with a 5 A buffer
                           # about their current camera positions

PYMOL API

   cmd.clip( string mode, float distance, string selection = None)

SEE ALSO

   zoom, reset


cls

DESCRIPTION

   "cls" clears the output buffer.

USAGE

   cls


color

DESCRIPTION

   "color" changes the color of an object or an atom selection.

USAGE

   color color-name
   color color-name, object-name
   color color-name, (selection)

PYMOL API

   cmd.color( string color, string color-name )

EXAMPLES 

   color yellow, (name C*)


commands

COMMANDS

   INPUT/OUTPUT  load      save      delete    quit
   VIEW          turn      move      clip      rock
                 show      hide      enable    disable
                 reset     refresh   rebuild   
                 zoom      origin    orient   
                 view      get_view  set_view
   MOVIES        mplay     mstop     mset      mdo
                 mpng      mmatrix   frame
                 rewind    middle    ending
                 forward   backward
   IMAGING       png       mpng
   RAY TRACING   ray       
   MAPS          isomesh   isodot
   DISPLAY       cls       viewport  splash    
   SELECTIONS    select    mask   
   SETTINGS      set       button
   ATOMS         alter     alter_state 
   EDITING       create    replace   remove    h_fill   remove_picked
                 edit      bond      unbond    h_add    fuse       
                 undo      redo      protect   cycle_valence  attach
   FITTING       fit       rms       rms_cur   pair_fit  
                 intra_fit intra_rms intra_rms_cur   
   COLORS        color     set_color
   HELP          help      commands
   DISTANCES     dist      
   STEREO        stereo
   SYMMETRY      symexp
   SCRIPTS       @         run
   LANGUAGE      alias     extend

Try "help <command-name>".  Also see the following extra topics:

   "movies", "keyboard", "mouse", "selections",
   "examples", "launching", "editing", and "api".


copy

DESCRIPTION

   "copy" creates a new object that is an identical copy of an
   existing object

USAGE

   copy target, source

   copy target = source         # (DEPRECATED)

PYMOL API

   cmd.copy(string target,string source)

SEE ALSO

   create


count_atoms

DESCRIPTION

   "count_atoms" returns a count of atoms in a selection.

USAGE

   count_atoms (selection)

PYMOL API

   cmd.count(string selection)


count_frames

DESCRIPTION

   "count_frames" is an API-only function which returns the number of
   frames defined for the PyMOL movie.

PYMOL API

   cmd.count_frames()

SEE ALSO

   frame, count_states


count_states

DESCRIPTION

   "count_states" is an API-only function which returns the number of
   states in the selection.

PYMOL API

   cmd.count_states(string selection="(all)")

SEE ALSO

   frame


create

DESCRIPTION

   "create" creates a new molecule object from a selection.  It can
   also be used to create states in an existing object.

   NOTE: this command has not yet been throughly tested.

USAGE

   create name, (selection) [,source_state [,target_state ] ]

   create name = (selection) [,source_state [,target_state ] ]
     # (DEPRECATED)

   name = object to create (or modify)
   selection = atoms to include in the new object
   source_state (default: 0 - copy all states)
   target_state (default: 0)

PYMOL API

   cmd.create(string name, string selection, int state, int target_state)

NOTES

   If the source and target states are zero (default), all states will
   be copied.  Otherwise, only the indicated states will be copied.

SEE ALSO

   load, copy


ctrl_special

dict() -> new empty dictionary.
dict(mapping) -> new dictionary initialized from a mapping object's
    (key, value) pairs.
dict(seq) -> new dictionary initialized as if via:
    d = {}
    for k, v in seq:
        d[k] = v


cycle_valence

DESCRIPTION

   "cycle_valence" cycles the valence on the currently selected bond.

USAGE

   cycle_valence [ h_fill ]

PYMOL API

   cmd.cycle_valence(int h_fill)

EXAMPLES

   cycle_valence
   cycle_valence 0

NOTES

   If the h_fill flag is true, hydrogens will be added or removed to
   satisfy valence requirements.

   This function is usually connected to the DELETE key and "CTRL-W".

SEE ALSO

   remove_picked, attach, replace, fuse, h_fill


decline

SECURITY FEATURE


delete

DESCRIPTION

   "delete" removes an object or a selection. 

USAGE

   delete name  
   delete all   # deletes all objects

   name = name of object or selection

PYMOL API

   cmd.delete (string name = object-or-selection-name )

SEE ALSO

   remove


deprotect

DESCRIPTION

   "deprotect" reveres the effect of the "protect" command.

USAGE

   deprotect (selection)

PYMOL API

   cmd.deprotect(string selection="(all)")

SEE ALSO

   protect, mask, unmask, mouse, editing


deselect

DESCRIPTION

   "deselect" disables any and all visible selections

USAGE

   deselect

PYMOL API

   cmd.deselect()


disable

DESCRIPTION

   "disable" disables display of an object and all currently visible
   representations.

USAGE

   disable name
   disable all 

   "name" is the name of an object or a named selection

PYMOL API

   cmd.disable( string name ) 

EXAMPLE

   disable my_object

SEE ALSO

   show, hide, enable


distance

DESCRIPTION

   "distance" creates a new distance object between two
   selections.  It will display all distances within the cutoff.

USAGE

   distance 
   distance (selection1), (selection2)
   distance name = (selection1), (selection1) [,cutoff [,mode] ]

   name = name of distance object 
   selection1,selection2 = atom selections
   cutoff = maximum distance to display
   mode = 0 (default)

PYMOL API

   cmd.distance( string name, string selection1, string selection2,
          string cutoff, string mode )
   returns the average distance between all atoms/frames

NOTES

   The distance wizard makes measuring distances easier than using
   the "dist" command for real-time operations.

   "dist" alone will show distances between selections (lb) and (rb)
   created by left and right button atom picks.  CTRL-SHIFT/left-click
   on the first atom,  CTRL-SHIFT/right-click on the second, then run
   "dist".


do

DESCRIPTION

   "do" makes it possible for python programs to issue simple PyMOL
   commands as if they were entered on the command line.

PYMOL API

   cmd.do( commands )

USAGE (PYTHON)

   from pymol import cmd
   cmd.do("load file.pdb")


dss

DESCRIPTION

   "dss" defines secondary structure based on backbone geometry
   and hydrogen bonding patterns.

   With PyMOL, heavy emphasis is placed on cartoon aesthetics, and so
   both hydrogen bonding patterns and backbone geometry are used in
   the assignment process.  Depending upon the local context, helix
   and strand assignments are made based on geometry, hydrogen
   bonding, or both.

   This command will generate results which differ slightly from DSSP
   and other programs.  Most deviations occur in borderline or
   transition regions.  Generally speaking, PyMOL is more strict, thus
   assigning fewer helix/sheet residues, except for partially
   distorted helices, which PyMOL tends to tolerate.
   
   WARNING: This algorithm has not yet been rigorously validated.
   
USAGE

   dss selection, state

   state = state-index or 0 for all states
   
EXAMPLES

   dss

NOTES

   If you dislike one or more of the assignments made by dss, you can
   use the alter command to make changes (followed by "rebuild").
   For example:
   
      alter 123-125/, ss='L'
      alter pk1, ss='S'
      alter 90/, ss='H'
      rebuild


dummy

DESCRIPTION

   This is a dummy function which returns None.


edit

DESCRIPTION

   "edit" picks an atom or bond for editing.

USAGE

   edit (selection) [ ,(selection) ]

PYMOL API

   cmd.edit( string selection  [ ,string selection ] )

NOTES

   If only one selection is provided, an atom is picked.
   If two selections are provided, the bond between them
   is picked (if one exists).

SEE ALSO

   unpick, remove_picked, cycle_valence, torsion


enable

DESCRIPTION

   "enable" enable display of an object and all currently visible representations.

USAGE

   enable name
   enable all

   name = object or selection name

PYMOL API

   cmd.enable( string object-name )

EXAMPLE

   enable my_object

SEE ALSO

   show, hide, disable


ending

DESCRIPTION

   "ending" goes to the end of the movie.

USAGE

   ending

PYMOL API

   cmd.ending()


extend

DESCRIPTION

   "extend" is an API-only function which binds a new external
   function as a command into the PyMOL scripting language.

PYMOL API

   cmd.extend(string name,function function)

PYTHON EXAMPLE

   def foo(moo=2): print moo
   cmd.extend('foo',foo)

   The following would now work within PyMOL:

   PyMOL>foo
   2
   PyMOL>foo 3
   3
   PyMOL>foo moo=5
   5
   PyMOL>foo ?
   Usage: foo [ moo ]

NOTES

   For security reasons, new PyMOL commands created using "extend" are
   not saved or restored in sessions.
   
SEE ALSO

   alias, api


feedback

DESCRIPTION

   "feedback" allows you to change the amount of information output by pymol.

USAGE

   feedback action,module,mask

   action is one of ['set','enable','disable']
   module is a space-separated list of strings or simply "all"
   mask is a space-separated list of strings or simply "everything"

NOTES:

   "feedback" alone will print a list of the available module choices

PYMOL API

   cmd.feedback(string action,string module,string mask)

EXAMPLES

   feedback enable, all , debugging
   feedback disable, selector, warnings actions
   feedback enable, main, blather

DEVELOPMENT TO DO

   Add a way of querying the current feedback settings.
   Check C source code to make source correct modules are being used.
   Check C source code to insure that all output is properly
   Update Python API and C source code to use "quiet" parameter as well.


find_pairs

DESCRIPTION

   "find_pairs" is currently undocumented.


fit

DESCRIPTION

   "fit" superimposes the model in the first selection on to the model
   in the second selection.  Only matching atoms in both selections
   will be used for the fit.

USAGE

   fit (selection), (target-selection)

EXAMPLES

   fit ( mutant and name ca ), ( wildtype and name ca )

SEE ALSO

   rms, rms_cur, intra_fit, intra_rms, intra_rms_cur


flag

DESCRIPTION

   "flag" sets the indicated flag for atoms in the selection and
    clears the indicated flag for atoms not in the selection.  This
    is primarily useful for passing selection information into
    Chempy models, which have a 32 bit attribute "flag" which holds
    this information.

USAGE

   flag flag, selection [ ,action ]

   flag flag = selection [ ,action ]      # (DEPRECATED)

   action can be:
     "reset" (default) sets flag on selection, clear it on other atoms 
     "set" sets the flag for selected atoms, leaves other atoms unchanged
     "clear" clear the flag for selected atoms, leaves other atoms unchanged

PYMOL API

   cmd.flag( int flag, string selection, string action="reset",
             int indicate=0)
   cmd.flag( string flag, string selection, string action="reset",
             int indicate=0)

EXAMPLES  

   flag free, (resi 45 x; 6)

NOTE

   If the 'auto_indicate_flags' setting is true, then PyMOL will automatically
   create a selection called "indicate" which contains all atoms with that flag
   after applying the command.

RESERVED FLAGS

   Flags 0-7 are reserved for molecular modeling */
      focus      0 = Atoms of Interest (i.e. a ligand in an active site)
      free       1 = Free Atoms (free to move subject to a force-field)
      restrain   2 = Restrained Atoms (typically harmonically contrained)
      fix        3 = Fixed Atoms (no movement allowed)
      exclude    4 = Atoms which should not be part of any simulation
   Flags 8-15 are free for end users to manipulate
   Flags 16-23 are reserved for external GUIs and linked applications
   Flags 24-31 are reserved for PyMOL internal usage
      exfoliate 24 = Remove surface from atoms when surfacing
      ignore    25 = Ignore atoms altogether when surfacing
      no_smooth 26 = Don't smooth atom position


forward

DESCRIPTION

   "forward" moves the movie one frame forward.

USAGE

   forward

PYMOL API

   cmd.forward()

SEE ALSO

   mset, backward, rewind


fragment

DESCRIPTION

   "fragment" retrieves a 3D structure from the fragment library, which is currently
   pretty meager (just amino acids).

USAGE

   fragment name


frame

DESCRIPTION

   "frame" sets the viewer to the indicated movie frame.

USAGE

   frame frame-number

PYMOL API

   cmd.frame( int frame_number )

NOTES

   Frame numbers are 1-based

SEE ALSO

   count_states


full_screen

DESCRIPTION

   "full_screen" enables or disables PyMOL's full screen mode.  This
   does not work well on all platforms.  

USAGE

   full_screen on
   full_screen off


fuse

DESCRIPTION

   "fuse" joins two objects into one by forming a bond.  A copy of
   the object containing the first atom is moved so as to form an
   approximately resonable bond with the second, and is then merged
   with the first object.

USAGE

   fuse (selection1), (selection2)

PYMOL API

   cmd.fuse( string selection1="(lb)", string selection2="(lb)" )

NOTES

   Each selection must include a single atom in each object.
   The atoms can both be hydrogens, in which case they are
   eliminated, or they can both be non-hydrogens, in which
   case a bond is formed between the two atoms.

SEE ALSO

   bond, unbond, attach, replace, fuse, remove_picked


get_area

PRE-RELEASE functionality - API will change


get_chains

PRE-RELEASE functionality - API will change

      state is currently ignored


get_dihedral

DESCRIPTION

   "get_dihedral" returns the dihedral angle between four atoms.  By
   default, the coordinates used are from the current state, however
   an alternate state identifier can be provided.

   By convention, positive dihedral angles are right-handed
   (looking down the atom2-atom3 axis).

USAGE

   get_dihedral atom1, atom2, atom3, atom4 [,state ]

EXAMPLES

   get_dihedral 4/n,4/c,4/ca,4/cb
   get_dihedral 4/n,4/c,4/ca,4/cb,state=4

PYMOL API

   cmd.get_dihedral(atom1,atom2,atom3,atom4,state=0)


get_extent

DESCRIPTION

   "get_extent" returns the minimum and maximum XYZ coordinates of a
   selection as an array:
    [ [ min-X , min-Y , min-Z ],[ max-X, max-Y , max-Z ]]

PYMOL API

   cmd.get_extent(string selection="(all)", state=0 )


get_frame

DESCRIPTION

   "get_frame" returns the current frame index (1-based)

PYMOL API

   Frames refers to sequences of images in a movie.  Sequential frames
   may contain identical molecular states, they may have one-to-one
   correspondance to molecular states (default), or they may have an
   arbitrary relationship, specific using the "mset" command.

SEE ALSO

   get_state


get_model

DESCRIPTION

   "get_model" returns a ChemPy "Indexed" format model from a selection.

PYMOL API

   cmd.get_model(string selection [,int state] )


get_names

DESCRIPTION

   "get_names" returns a list of object and/or selection names.

PYMOL API

   cmd.get_names( [string: "objects"|"selections"|"all"] )

NOTES

   The default behavior is to return only object names.

SEE ALSO

   get_type, count_atoms, count_states


get_pdbstr

DESCRIPTION

   "get_pdbstr" in an API-only function which returns a pdb
   corresponding to the atoms in the selection provided and that are
   present in the indicated state

PYMOL API ONLY

   cmd.get_pdbstr( string selection="all", int state=0 )

NOTES

   "state" is a 1-based state index for the object.

   if state is zero, then current state is used.


get_povray

DESCRIPTION

   "get_povray" returns a tuple corresponding to strings for a PovRay
   input file.

PYMOL API

   cmd.get_povray()


get_state

DESCRIPTION

   "get_state" returns the current state index (1-based)

PYMOL API

   cmd.get_state()

NOTES

   States refer to different geometric configurations which an object
   can above.  By default, states and movie frames have a one-to-one
   relationship.  States can be visited in an arbitrary order to
   create frames.  The "mset" command allows you to build a
   relationship between states and frames.

SEE ALSO

   get_frame


get_symmetry

DESCRIPTION

   "get_symmetry" can be used to obtain the crystal
   and spacegroup parameters for a molecule
   (FUTURE - map object - FUTURE)

USAGE

   get_symmetry object-name-or-selection

PYMOL API

   cmd.get_symmetry(string selection)


get_title

DESCRIPTION

   "get_title" retrieves a text string to the state of a particular
   object which will be displayed when the state is active.

USAGE

   set_title object,state

PYMOL API

   cmd.set_title(string object,int state,string text)


get_type

DESCRIPTION

   "get_type" returns a string describing the named object or
    selection or the string "nonexistent" if the name in unknown.

PYMOL API

   cmd.get_type(string object-name)

NOTES

   Possible return values are

   "object:molecule"
   "object:map"
   "object:mesh"
   "object:distance"
   "selection"

SEE ALSO

   get_names


get_view

DESCRIPTION

   "get_view" returns and optionally prints out the current view
   information in a format which can be embedded into a command
   script and can be used in subsequent calls to "set_view".

   If a log file is currently open, get_view will not write the view
   matrix to the screen unless the "output" parameter is 2.

USAGE

   get_view

PYMOL API

   cmd.get_view(output=1,quiet=1)
   
   my_view= cmd.get_view()

   output control:
   
      0 = output matrix to screen
      1 = don't output matrix to screen
      2 = force output to screen even if log file is open
      
API USAGE

   cmd.get_view(0) # zero option suppresses output (LEGACY approach)
   cmd.get_view(quiet=1) # suppresses output using PyMOL's normal "quiet" parameter.

NOTES

   Contents of the view matrix
      0  -  8 = 3x3 rotation matrix which transforms model to camera space
      9  - 11 = camera position (in model space and relative to the origin of rotation)
      12 - 14 = origin of rotation (in model space)
      15      = front plane distance from the camera
      16      = rear plane distance from the camera
      17      = orthoscopic flag 

SEE ALSO

   set_view


h_add

DESCRIPTION

   "h_add" uses a primitive algorithm to add hydrogens
   onto a molecule.

USAGE

   h_add (selection)

PYMOL API

   cmd.h_add( string selection="(all)" )

SEE ALSO

   h_fill


h_fill

DESCRIPTION

   "h_fill" removes and replaces hydrogens on the atom
   or bond picked for editing.  

USAGE

   h_fill

PYMOL API

   cmd.h_fill()

NOTES

   This is useful for fixing hydrogens after changing
   bond valences.

SEE ALSO

   edit, cycle_valence, h_add


help

DESCRIPTION

   "help" prints out the online help for a given command.

USAGE

   help command


hide

DESCRIPTION

   "hide" turns of atom and bond representations.

   The available representations are:

      lines     spheres   mesh      ribbon     cartoon
      sticks    dots      surface   labels
      nonbonded nb_spheres

USAGE

   hide reprentation [,object]
   hide reprentation [,(selection)]
   hide (selection)

PYMOL API

   cmd.hide( string representation="", string selection="")

EXAMPLES

   hide lines,all
   hide ribbon

SEE ALSO

   show, enable, disable


id_atom

DESCRIPTION

   "id_atom" returns the original source id of a single atom, or
   raises and exception if the atom does not exist or if the selection
   corresponds to multiple atoms.

PYMOL API

   list = cmd.id_atom(string selection)


identify

DESCRIPTION

   "identify" returns a list of atom IDs corresponding to the ID code
   of atoms in the selection.

PYMOL API

   list = cmd.identify(string selection="(all)",int mode=0)

NOTES

   mode 0: only return a list of identifiers (default)
   mode 1: return a list of tuples of the object name and the identifier


index

DESCRIPTION

   "index" returns a list of tuples corresponding to the
   object name and index of the atoms in the selection.

PYMOL API

   list = cmd.index(string selection="(all)")

NOTE

  Atom indices are fragile and will change as atoms are added
  or deleted.  Whenever possible, use integral atom identifiers
  instead of indices.


indicate

DESCRIPTION

   "indicate" shows a visual representation of an atom selection.

USAGE

   indicate (selection)

PYMOL API

   cmd.count(string selection)


intra_fit

DESCRIPTION

   "intra_fit" fits all states of an object to an atom selection
   in the specified state.  It returns the rms values to python
   as an array.

USAGE 

   intra_fit (selection),state

PYMOL API

   cmd.intra_fit( string selection, int state )

EXAMPLES

   intra_fit ( name ca )

PYTHON EXAMPLE

   from pymol import cmd
   rms = cmd.intra_fit("(name ca)",1)

SEE ALSO

   fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit


intra_rms

DESCRIPTION

   "intra_rms" calculates rms fit values for all states of an object
   over an atom selection relative to the indicated state.  
   Coordinates are left unchanged.  The rms values are returned
   as a python array.

PYMOL API

   cmd.intra_rms( string selection, int state)

PYTHON EXAMPLE

   from pymol import cmd
   rms = cmd.intra_rms("(name ca)",1)

SEE ALSO

   fit, rms, rms_cur, intra_fit, intra_rms_cur, pair_fit


intra_rms_cur

DESCRIPTION

   "intra_rms_cur" calculates rms values for all states of an object
   over an atom selection relative to the indicated state without
   performing any fitting.  The rms values are returned
   as a python array.

PYMOL API

   cmd.intra_rms_cur( string selection, int state)

PYTHON EXAMPLE

   from pymol import cmd
   rms = cmd.intra_rms_cur("(name ca)",1)

SEE ALSO

   fit, rms, rms_cur, intra_fit, intra_rms, pair_fit


invert

DESCRIPTION

   "invert" inverts the stereo-chemistry of the atom currently picked
   for editing (pk1).  Two additional atom selections must be provided
   in order to indicate which atoms remain stationary during the
   inversion process.

USAGE

   invert (selection1),(selection2)

PYMOL API

   cmd.api( string selection1="(lb)", string selection2="(lb)" )

NOTE

   The invert function is usually bound to CTRL-E in editing mode.

   The default selections are (lb) and (rb), meaning that you can pick
   the atom to invert with CTRL-middle click and then pick the
   stationary atoms with CTRL-SHIFT/left-click and CTRL-SHIFT/right-
   click, then hit CTRL-E to invert the atom.


isodot

DESCRIPTION

   "isodot" creates a dot isosurface object from a map object.

USAGE

   isodot name = map, level [,(selection) [,buffer [, state ] ] ] 

   map = the name of the map object to use.

   level = the contour level.

   selection = an atom selection about which to display the mesh with
      an additional "buffer" (if provided).

NOTES

   If the dot isosurface object already exists, then the new dots will
   be appended onto the object as a new state.

SEE ALSO

   load, isomesh


isolevel

DESCRIPTION

   "isolevel" changes the contour level of a isodot, isosurface, or isomesh object.

USAGE

   isolevel name, level, state


isomesh

DESCRIPTION

   "isomesh" creates a mesh isosurface object from a map object.

USAGE

   isomesh name, map, level [,(selection) [,buffer [,state [,carve ]]]]

   name = the name for the new mesh isosurface object.

   map = the name of the map object to use for computing the mesh.

   level = the contour level.

   selection = an atom selection about which to display the mesh with
      an additional "buffer" (if provided).

   state = the state into which the object should be loaded (default=1)
      (set state=0 to append new mesh as a new state)

   carve = a radius about each atom in the selection for which to
      include density. If "carve" is not provided, then the whole
      brick is displayed.

NOTES

   If the mesh object already exists, then the new mesh will be
   appended onto the object as a new state (unless you indicate a state).

   state > 0: specific state
   state = 0: all states
   state = -1: current state
   
   source_state > 0: specific state
   source_state = 0: include all states starting with 0
   source_state = -1: current state
   source_state = -2: last state in map

SEE ALSO

   isodot, load


isosurface

DESCRIPTION

   "isosurface" creates a new surface object from a map object.

USAGE

   isosurface name, map, level [,(selection) [,buffer [,state [,carve ]]]]

   name = the name for the new mesh isosurface object.

   map = the name of the map object to use for computing the mesh.

   level = the contour level.

   selection = an atom selection about which to display the mesh with
      an additional "buffer" (if provided).

   state = the state into which the object should be loaded (default=1)
      (set state=0 to append new surface as a new state)

   carve = a radius about each atom in the selection for which to
      include density. If "carve= not provided, then the whole
      brick is displayed.

NOTES

   If the surface object already exists, then the new surface will be
   appended onto the object as a new state (unless you indicate a state).

SEE ALSO

   isodot, isomesh, load


iterate

DESCRIPTION

   "iterate" iterates over an expression with a separate name space
   for each atom.  However, unlike the "alter" command, atomic
   properties can not be altered.  Thus, "iterate" is more efficient
   than "alter".

   It can be used to perform operations and aggregations using atomic
   selections, and store the results in any global object, such as the
   predefined "stored" object.

   The local namespace for "iterate" contains the following names

      name, resn, resi, chain, alt, elem,
      q, b, segi, and type (ATOM,HETATM),
      partial_charge, formal_charge,
      text_type, numeric_type, ID

   All strings in the expression must be explicitly quoted.  This
   operation typically takes a second per thousand atoms.

USAGE

   iterate (selection),expression

EXAMPLES

   stored.net_charge = 0
   iterate (all),stored.net_charge = stored.net_charge + partial_charge

   stored.names = []
   iterate (all),stored.names.append(name)

SEE ALSO

   iterate_state, atler, alter_state


iterate_state

DESCRIPTION

   "iterate_state" is to "alter_state" as "iterate" is to "alter"

USAGE

   iterate_state state,(selection),expression

EXAMPLES

   stored.sum_x = 0.0
   iterate 1,(all),stored.sum_x = stored.sum_x + x

SEE ALSO

   iterate, alter, alter_state


keyword

dict() -> new empty dictionary.
dict(mapping) -> new dictionary initialized from a mapping object's
    (key, value) pairs.
dict(seq) -> new dictionary initialized as if via:
    d = {}
    for k, v in seq:
        d[k] = v


label

DESCRIPTION

   "label" labels one or more atoms properties over a selection using
   the python evaluator with a separate name space for each atom.  The
   symbols defined in the name space are:

      name, resn, resi, chain, q, b, segi, type (ATOM,HETATM) 
      formal_charge, partial_charge, numeric_type, text_type

   All strings in the expression must be explicitly quoted.  This
   operation typically takes several seconds per thousand atoms
   altered.

   To clear labels, simply omit the expression or set it to ''.

USAGE

   label (selection),expression

EXAMPLES

   label (chain A),chain
   label (n;ca),"%s-%s" % (resn,resi)
   label (resi 200),"%1.3f" % partial_charge


load

DESCRIPTION

   "load" reads several file formats.  The file extension is used to
   determine the format.  PDB files must end in ".pdb", MOL files must
   end in ".mol", Macromodel files must end in ".mmod", XPLOR
   maps must end in ".xplor", CCP4 maps must end in ".ccp4",
   Raster3D input (Molscript output) must end in ".r3d", PyMOL session
   files must end in ".pse"

   Pickled ChemPy models with a ".pkl" can also be directly read.

   If an object is specified, then the file is loaded into that object.
   Otherwise, an object is created with the same name as the file
   prefix.

USAGE

   load filename [,object [,state [,format [,finish [,discrete ]]]]]

PYMOL API

   cmd.load( filename [,object [,state [,format [,finish [,discrete ]]]]]

NOTES

   You can override the file extension by giving a format string:

   'pdb' : PDB,  'mmod' : Macromodel, 'xyz' : Tinker, 'cc1' : ChemDraw3D  
   'mol' : MDL MOL-file, 'sdf' : MDL SD-file
   'xplor' : X-PLOR/CNS map, 'ccp4' : CCP4 map,
   'callback' : PyMOL Callback object (PyOpenGL)
   'cgo' : compressed graphics object (list of floats)
   'trj' : AMBER trajectory (use load_traj command for more control)
   'top' : AMBER topology file 'rst' : AMBER restart file
   'cex' : Metaphorics CEX format
   'pse' : PyMOL Session file

SEE ALSO

   save


load_brick

Temporary routine for GAMESS-UK project.


load_callback

DESCRIPTION

   "load_callback" is used to load a generic Python callback object.
   These objects are called every time the screen is updated and can be used
   to trigger OpenGL rendering calls (such as with PyOpenGL).

PYMOL API

   cmd.load_callback(object,name,state,finish,discrete)


load_cgo

DESCRIPTION

   "load_cgo" is used to load a compiled graphics object, which is
   actually a list of floating point numbers built using the constants
   in the $PYMOL_PATH/modules/pymol/cgo.py file.

PYMOL API

   cmd.load_cgo(object,name,state,finish,discrete)


load_map

Temporary routine for the Phenix project.


load_model

DESCRIPTION

   "load_model" reads a ChemPy model into an object

PYMOL API

   cmd.load_model(model, object [,state [,finish [,discrete ]]])


load_object

DESCRIPTION

   "load_object" is a general developer function for loading Python objects
   into PyMOL.

PYMOL API

   cmd.load_object(type,object,name,state=0,finish=1,discrete=0)

   type = one one of the numberic cmd.loadable types
   object =
   name = object name (string)
   finish = perform (1) or defer (0) post-processing of structure after load
   discrete = treat each state as an independent, unrelated set of atoms


load_traj

DESCRIPTION

   "load_traj" reads trajectory files (currently just AMBER files).
   The file extension is used to determine the format.

   AMBER files must end in ".trj" 

USAGE

   load_traj filename [,object [,state [,format [,interval [,average ]
                      [,start [,stop [,max [,selection [,image [,shift
                      ]]]]]]]]]

PYMOL API

   cmd.load_traj(filename,object='',state=0,format='',interval=1,
              average=1,start=1,stop=-1,max=-1,selection='all',image=1,
              shift="[0.0,0.0,0.0]")

NOTES

   You must first load a corresponding topology file before attempting
   to load a trajectory file.

   PyMOL does not know how to wrap the truncated octahedron used by Amber
   You will need to use the "ptraj" program first to do this.

   The average option is not a running average.  To perform this type of
   average, use the "smooth" command after loading the trajectory file.

SEE ALSO

   load


ls

DESCRIPTION

   List contents of the current working directory.

USAGE

   ls [pattern]
   dir [pattern]

EXAMPLES

   ls
   ls *.pml

SEE ALSO

   cd, pwd, system


map_double

DESCRIPTION

   "map_double" resamples a map at twice the current resolution.  The
   amount of memory required to store the map will increase
   eight-fold.

USAGE

   map_double map_name, state


map_new

state > 0: do indicated state
      state = 0: independent states in independent extents
      state = -1: current state
      state = -2: independent states in unified extent
      state = -3: all states in one map


map_set_border

DESCRIPTION

   "map_set_border" is a function (reqd by PDA) which allows you to set the
   level on the edge points of a map

USAGE

   map_set_border <name>,<level>

NOTES

   unsupported.
   
SEE ALSO

   load


mappend

DESCRIPTION

USAGE

   mappend frame : command

PYMOL API

EXAMPLE

NOTES

SEE ALSO

   mset, mplay, mstop


mask

DESCRIPTION

   "mask" makes it impossible to select the indicated atoms using the
   mouse.  This is useful when you are working with one molecule in
   front of another and wish to avoid accidentally selecting atoms in
   the background.

USAGE

   mask (selection)

PYMOL API

   cmd.mask( string selection="(all)" )

SEE ALSO

   unmask, protect, deprotect, mouse


mclear

DESCRIPTION

   "mclear" clears the movie frame image cache.

USAGE

   mclear

PYMOL API

   cmd.mclear()


mdo

DESCRIPTION

   "mdo" sets up a command to be executed upon entry into the
   specified frame of the movie.  These commands are usually created
   by a PyMOL utility program (such as util.mrock).  Command can
   actually contain several commands separated by semicolons ';'

USAGE

   mdo frame : command

PYMOL API

   cmd.mdo( int frame, string command )

EXAMPLE

   // Creates a single frame movie involving a rotation about X and Y

   load test.pdb
   mset 1
   mdo 1, turn x,5; turn y,5;
   mplay

NOTES

   The "mset" command must first be used to define the movie before
   "mdo" statements will have any effect.  Redefinition of the movie
   clears any existing mdo statements.

SEE ALSO

   mset, mplay, mstop


mdump

DESCRIPTION

   "mdump" dumps the current set of movie commands

USAGE

   mdump

PYMOL API

   cmd.mdump()

SEE ALSO

   mplay, mset, mdo, mclear, mmatrix


mem

DESCRIPTION

   "mem" Dumps current memory state to standard output. This is a
   debugging feature, not an official part of the API.


meter_reset

DESCRIPTION

   "meter_reset" resets the frames per secound counter

USAGE

   meter_reset


middle

DESCRIPTION

   "middle" goes to the middle of the movie.

USAGE

   middle

PYMOL API

   cmd.middle()


mmatrix

DESCRIPTION

   "mmatrix" sets up a matrix to be used for the first frame of the movie.

USAGE

   mmatrix {clear|store|recall}

PYMOL API

   cmd.mmatrix( string action )

EXAMPLES

   mmatrix store


move

DESCRIPTION

   "move" translates the camera about one of the three primary axes.

USAGE

   move axis,distance

EXAMPLES

   move x,3
   move y,-1

PYMOL API

   cmd.move( string axis, float distance )

SEE ALSO

   turn, rotate, translate, zoom, center, clip


mplay

DESCRIPTION

   "mplay" starts the movie.

USAGE

   mplay

PYMOL API

   cmd.mplay()

SEE ALSO

   mstop, mset, mdo, mclear, mmatrix


mpng

DESCRIPTION

   "mpng" writes a series of numbered movie frames to png files with
   the specified prefix.  If the "ray_trace_frames" variable is
   non-zero, these frames will be ray-traced.  This operation can take
   several hours for a long movie.

   Be sure to disable "cache_frames" when issuing this operation on a
   long movie (>100 frames) to avoid running out of memory.

USAGE

   mpng prefix [, first [, last]]

   Options "first" and "last" can be used to specify an inclusive
   interval over which to render frames.  Thus, you can write a smart
   Python program that will automatically distribute rendering over a
   cluster of workstations.  If these options are left at zero, then
   the entire movie will be rendered.

PYMOL API

   cmd.mpng( string prefix, int first=0, int last=0 )


mset

DESCRIPTION

   "mset" sets up a relationship between molecular states and movie
   frames.  This makes it possible to control which states are shown
   in which frame.

USAGE

   mset specification

PYMOL API

   cmd.mset( string specification )

EXAMPLES

   mset 1         // simplest case, one state -> one frame
   mset 1 x10     // ten frames, all corresponding to state 1
   mset 1 x30 1 -15 15 x30 15 -1
     // more realistic example:
     // the first thirty frames are state 1
     // the next 15 frames pass through states 1-15
     // the next 30 frames are of state 15
     // the next 15 frames iterate back to state 1

SEE ALSO

   mdo, mplay, mclear


mstop

DESCRIPTION

   "mstop" stops the movie.

USAGE

   mstop

PYMOL API

   cmd.mstop()

SEE ALSO

   mplay, mset, mdo, mclear, mmatrix


orient

DESCRIPTION

   "orient" aligns the principal components of the atoms in the
   selection with the XYZ axes.  The function is similar to the
   orient command in X-PLOR.

USAGE

   orient object-or-selection [, state]
   orient (selection)

PYMOL API

   cmd.orient( string object-or-selection [, state = 0] )

NOTES

   state = 0 (default) use all coordinate states
   state = -1 use only coordinates for the current state
   state > 0  use coordinates for a specific state

SEE ALSO

   zoom, origin, reset


origin

DESCRIPTION

   "origin" sets the center of rotation about a selection.
   If an object name is specified, it can be used to set
   the center of rotation for the object's TTT matrix.

USAGE

   origin selection [, object [,position, [, state]]]
   origin (selection)
   origin position=[1.0,2.0,3.0]

PYMOL API

   cmd.origin( string object-or-selection )

NOTES

   state = 0 (default) use all coordinate states
   state = -1 use only coordinates for the current state
   state > 0  use coordinates for a specific state

SEE ALSO

   zoom, orient, reset


pair_fit

DESCRIPTION

   "pair_fit" fits a set of atom pairs between two models.  Each atom
   in each pair must be specified individually, which can be tedious
   to enter manually.  Script files are recommended when using this
   command.

USAGE

   pair_fit (selection), (selection), [ (selection), (selection) [ ...] ]

SEE ALSO

   fit, rms, rms_cur, intra_fit, intra_rms, intra_rms_cur


png

DESCRIPTION

   "png" writes a png format image file of the current image to disk.

USAGE

   png filename

PYMOL API

   cmd.png( string file )


protect

DESCRIPTION

   "protect" protects a set of atoms from tranformations performed
   using the editing features.  This is most useful when you are
   modifying an internal portion of a chain or cycle and do not wish
   to affect the rest of the molecule.

USAGE

   protect (selection)

PYMOL API

   cmd.protect(string selection)

SEE ALSO

   deprotect, mask, unmask, mouse, editing


push_undo

DESCRIPTION

   "push_undo" stores the currently conformations of objects in the
   selection onto their individual kill rings.

USAGE

   push_undo (all)

SEE ALSO

   undo, redo


pwd

DESCRIPTION

   Print current working directory.

USAGE

   pwd

SEE ALSO

   cd, ls, system


quit

DESCRIPTION

   "quit" terminates the program. 

USAGE

   quit

PYMOL API

   cmd.quit()


ray

DESCRIPTION

   "ray" creates a ray-traced image of the current frame. This
   can take some time (up to several minutes, depending on image
   complexity).

USAGE

   ray [width,height [,renderer [,angle [,shift ]]]

   angle and shift can be used to generate matched stereo pairs
   
EXAMPLES

   ray
   ray 1024,768
   ray renderer=0

PYMOL API

   cmd.ray(int width,int height,int renderer=-1,float shift=0)

NOTES

   renderer = -1 is default (use value in ray_default_renderer)
   renderer =  0 uses PyMOL's internal renderer
   renderer =  1 uses PovRay's renderer.  This is Unix-only
      and you must have "x-povray" in your path.  It utilizes two
      two temporary files: "tmp_pymol.pov" and "tmp_pymol.png".

SEE ALSO

   "help faster" for optimization tips with the builtin renderer.
   "help povray" for how to use PovRay instead of PyMOL's built-in
   ray-tracing engine.


read_mmodstr

DESCRIPTION

   "read_mmodstr" reads a macromodel format structure from a Python
   string.


read_molstr

DESCRIPTION

   "read_molstr" reads an MDL MOL format file as a string

PYMOL API ONLY

   cmd.read_molstr( string molstr, string name, int state=0,
      int finish=1, int discrete=1 )

NOTES

   "state" is a 1-based state index for the object, or 0 to append.

   "finish" is a flag (0 or 1) which can be set to zero to improve
   performance when loading large numbers of objects, but you must
   call "finish_object" when you are done.

   "discrete" is a flag (0 or 1) which tells PyMOL that there will be
   no overlapping atoms in the file being loaded.  "discrete"
   objects save memory but can not be edited.


read_pdbstr

DESCRIPTION

   "read_pdbstr" in an API-only function which reads a pdb file from a
   Python string.  This feature can be used to load or update
   structures into PyMOL without involving any temporary files.

PYMOL API ONLY

   cmd.read_pdbstr( string pdb-content, string object name 
      [ ,int state [ ,int finish [ ,int discrete ] ] ] )

NOTES

   "state" is a 1-based state index for the object.

   "finish" is a flag (0 or 1) which can be set to zero to improve
   performance when loading large numbers of objects, but you must
   call "finish_object" when you are done.

   "discrete" is a flag (0 or 1) which tells PyMOL that there will be
   no overlapping atoms in the PDB files being loaded.  "discrete"
   objects save memory but can not be edited.


read_xplorstr

DESCRIPTION

   "read_xplorstr" in an API-only function which reads an XPLOR map
   from a Python string.  This feature can be used to bypass
   temporary files.

PYMOL API ONLY

   cmd.read_xplorstr( string xplor-content, string object name 
      [ ,int state ] )

NOTES

   "state" is a 1-based state index for the object.


rebuild

DESCRIPTION

   "rebuild" forces PyMOL to recreate geometric objects in
   case any of them have gone out of sync.

USAGE

   rebuild [selection [, representation ]]

PYMOL API

   cmd.rebuild(string selection = 'all', string representation = 'everything')

SEE ALSO

   refresh


recolor

DESCRIPTION

   "rebuild" forces PyMOL to reapply colors to geometric objects in
   case any of them have gone out of sync.

USAGE

   recolor [selection [, representation ]]

PYMOL API

   cmd.recolor(string selection = 'all', string representation = 'everything')

SEE ALSO

   recolor


redo

DESCRIPTION

   "redo" reapplies the conformational change of the object currently
   being edited.

USAGE

   redo

SEE ALSO

   undo, push_undo


refresh

DESCRIPTION

   "refresh" causes the scene to be refresh as soon as it is safe to
   do so.

USAGE

   refresh

PYMOL API

   cmd.refresh()

SEE ALSO

   rebuild


reinitialize

DESCRIPTION

   "reinitialize" reinitializes PyMOL

USAGE

   reinitialize


remove

DESCRIPTION

   "remove" eleminates a selection of atoms from models.

USAGE

   remove (selection)

PYMOL API

   cmd.remove( string selection )

EXAMPLES

   remove ( resi 124 )

SEE ALSO

   delete


remove_picked

DESCRIPTION

   "remove_picked" removes the atom or bond currently
   picked for editing. 

USAGE

   remove_picked [hydrogens]

PYMOL API

   cmd.remove_picked(integer hydrogens=1)

NOTES

   This function is usually connected to the
   DELETE key and "CTRL-D".

   By default, attached hydrogens will also be deleted unless
   hydrogen-flag is zero.

SEE ALSO

   attach, replace


rename

DESCRIPTION

   "rename" creates new atom names which are unique within residues.

USAGE

   CURRENT
      rename object-name [ ,force ]

      force = 0 or 1 (default: 0)

   PROPOSED
      rename object-or-selection,force   

PYMOL API

   CURRENT
      cmd.rename( string object-name, int force )

   PROPOSED
      cmd.rename( string object-or-selection, int force )

NOTES

   To regerate only some atom names in a molecule, first clear them
   with an "alter (sele),name=''" commmand, then use "rename"

SEE ALSO

   alter


replace

DESCRIPTION

   "replace" replaces the picked atom with a new atom.

USAGE

   replace element, geometry, valence [,h_fill [,name ]]

PYMOL API

   cmd.replace(string element, int geometry, int valence,
               int h_fill = 1, string name = "" )

NOTES

   Immature functionality. See code for details.

SEE ALSO

   remove, attach, fuse, bond, unbond


reset

DESCRIPTION

   "reset" restores the rotation matrix to identity, sets the origin
   to the center of mass (approx.) and zooms the window and clipping
   planes to cover all objects.

USAGE

   reset 

PYMOL API

   cmd.reset ( )


rewind

DESCRIPTION

   "rewind" goes to the beginning of the movie.

USAGE

   rewind

PYMOL API

   cmd.rewind()


rms

DESCRIPTION

   "rms" computes a RMS fit between two atom selections, but does not
   tranform the models after performing the fit.

USAGE

   rms (selection), (target-selection)

EXAMPLES

   fit ( mutant and name ca ), ( wildtype and name ca )

SEE ALSO

   fit, rms_cur, intra_fit, intra_rms, intra_rms_cur, pair_fit


rms_cur

DESCRIPTION

   "rms_cur" computes the RMS difference between two atom
   selections without performing any fitting.

USAGE

   rms_cur (selection), (selection)

SEE ALSO

   fit, rms, intra_fit, intra_rms, intra_rms_cur, pair_fit


rock

DESCRIPTION

   "rock" toggles Y axis rocking.

USAGE

   rock

PYMOL API

   cmd.rock()


rotate

DESCRIPTION

   "rotate" can be used to rotate the atomic coordinates of a
   molecular object.  Behavior differs depending on whether or not the
   "object" parameter is specified.

   If object is None, then rotate rotates the atomic coordinates
   according to the axes and angle for the selection and state
   provided.  All representation geometries will need to be
   regenerated to reflect the new atomic coordinates.

   If object is set to an object name, then selection and state are
   ignored and instead of translating the atomic coordinates, the
   object's representation display matrix is modified.  This option
   is for use in animations only.

USAGE

   rotate axis, angle [,selection [,state [,camera [,object [,origin]]]]]

PYMOL API

   cmd.rotate(list-or-string axis, string selection = "all", int state = 0,
              int camera = 1, string object = None)

EXAMPLES

   rotate x, 45, pept

NOTES

   if state = 0, then only visible state(s) are affected.
   if state = -1, then all states are affected.


save

DESCRIPTION

   "save" writes selected atoms to a file.  The file format is
   autodetected if the extesion is ".pdb", ".pse", ".mol", ".mmod", or
   ".pkl"

   Note that if the file extension ends in ".pse" (PyMOL Session), the
   complete PyMOL state is always saved to the file (the selection and
   state parameters are thus ignored).

USAGE

   save file [,(selection) [,state [,format]] ]

PYMOL API

   cmd.save(file, selection, state, format)

SEE ALSO

   load, get_model


scene

DESCRIPTION

   "scene" makes it possible to save and restore multiple scenes scene
   within a single session.  A scene consists of the view, all object
   activity information, all atom-wise visibility, color,
   representations, and the global frame index.  

USAGE

   scene key [,action [,message [ ,view [,color [,active [,rep [,frame]]]]]]]
   scene *

   key can be any string
   action should be 'store' or 'recall' (default: 'recall')

   view: 1 or 0 controls whether the view is stored
   color: 1 or 0 controls whether colors are stored
   active: 1 or 0 controls whether activity is stored
   rep: 1 or 0 controls whether the representations are stored
   frame: 1 or 0 controls whether the frame is stored
   
PYMOL API

   cmd.scene(string key,string action,string-or-list message,int view,
             int color, int active, int rep, int frame)

EXAMPLES

   scene F1 ,store
   scene F2, store, This view shows you the critical hydrogen bond.

   scene F1
   scene F2

NOTES

   Scenes F1 through F12 are automatically bound to function keys
   provided that "set_key" hasn't been used to redefine the behaviour
   of the respective key.
   
SEE ALSO

   view, set_view, get_view

DEVELOPMENT TO DO

   Add support for save/restore of a certain global and
      object-and-state specific settings, such as: state,
      surface_color, ribbon_color, stick_color, transparency,
      sphere_transparency, etc.  This would probably best be done by
      defining a class of "scene" settings which are treated in this
      manner.  The current workaround is to create separate objects
      which are enabled/disabled differentially.


sculpt_activate

undocumented.


sculpt_deactivate

undocumented


sculpt_iterate

undocumented.


sculpt_purge

undocumented


select

DESCRIPTION

   "select" creates a named selection from an atom selection.

USAGE

   select (selection)
   select name, (selection)
   select name = (selection)            # (DEPRECATED)

PYMOL API

   cmd.select(string name, string selection)

EXAMPLES 

   select near , (ll expand 8)
   select near , (ll expand 8)
   select bb, (name ca,n,c,o )

NOTES

   'help selections' for more information about selections.


set

DESCRIPTION

   "set" changes one of the PyMOL state variables,

USAGE

   set name, [,value [,object-or-selection [,state ]]]

   set name = value  # (DEPRECATED)

PYMOL API

   cmd.set ( string name, string value=1,
             string selection='', int state=0,
              int updates=1, quiet=1)

NOTES

   The default behavior (with a blank selection) changes the global
   settings database.  If the selection is 'all', then the settings
   database in all individual objects will be changed.  Likewise, for
   a given object, if state is zero, then the object database will be
   modified.  Otherwise, the settings database for the indicated state
   within the object will be modified.

   If a selection is provided, then all objects in the selection will
   be affected.


set_color

DESCRIPTION

   "set_color" defines a new color with color indices (0.0-1.0)

USAGE

   set_color name, [ red-float, green-float, blue-float ]

   set_color name = [ red-float, green-float, blue-float ]
     # (DEPRECATED)

PYMOL API

   cmd.set_color( string name, float-list rgb )

EXAMPLES 

   set_color red = [ 1.0, 0.0, 0.0 ]


set_geometry

DESCRIPTION

   "set_geometry" changes PyMOL's assumptions about the proper valence
   and geometry of the picked atom.

USAGE

   set_geometry geometry, valence

PYMOL API

   cmd.set_geometry(int geometry,int valence )

NOTES

   Immature functionality. See code for details.

SEE ALSO

   remove, attach, fuse, bond, unbond


set_key

DESCRIPTION

   "set_key" binds a specific python function to a key press.

PYMOL API (ONLY)

   cmd.set_key( string key, function fn, tuple arg=(), dict kw={})

PYTHON EXAMPLE

   from pymol import cmd

   def color_blue(object): cmd.color("blue",object)

   cmd.set_key( 'F1' , make_it_blue, ( "object1" ) )
   // would turn object1 blue when the F1 key is pressed and

   cmd.set_key( 'F2' , make_it_blue, ( "object2" ) )
   // would turn object2 blue when the F2 key is pressed.

   cmd.set_key( 'CTRL-C' , cmd.zoom )   
   cmd.set_key( 'ALT-A' , cmd.turn, ('x',90) )

KEYS WHICH CAN BE REDEFINED

   F1 to F12
   left, right, pgup, pgdn, home, insert
   CTRL-A to CTRL-Z 
   ALT-0 to ALT-9, ALT-A to ALT-Z

SEE ALSO

   button


set_symmetry

DESCRIPTION

   "set_symmetry" can be used to define or redefine the crystal
   and spacegroup parameters for a molecule or map object.

USAGE

   set_symmetry selection, a, b, c, alpha, beta, gamma, spacegroup

PYMOL API

   cmd.set_symmetry(string selection, float a, float b, float c,
        float alpha,float beta, float gamma, string spacegroup)

NOTES

   The new symmetry will be defined for every object referenced
   by the selection


set_title

DESCRIPTION

   "set_title" attaches a text string to the state of a particular
   object which can be displayed when the state is active.  This is
   useful for display the energies of a set of conformers.

USAGE

   set_title object,state,text

PYMOL API

   cmd.set_title(string object,int state,string text)


set_view

DESCRIPTION

   "set_view" sets viewing information for the current scene,
   including the rotation matrix, position, origin of rotation,
   clipping planes, and the orthoscopic flag.

USAGE

   set_view (...)  where ... is 18 floating point numbers

PYMOL API

   cmd.set_view(string-or-sequence view)  

SEE ALSO

   get_view


shft_special

dict() -> new empty dictionary.
dict(mapping) -> new dictionary initialized from a mapping object's
    (key, value) pairs.
dict(seq) -> new dictionary initialized as if via:
    d = {}
    for k, v in seq:
        d[k] = v


show

DESCRIPTION

   "show" turns on atom and bond representations.

   The available representations are:

      lines     spheres   mesh      ribbon     cartoon
      sticks    dots      surface   labels     extent
      nonbonded nb_spheres 

USAGE

   show
   show reprentation [,object]
   show reprentation [,(selection)]
   show (selection)

PYMOL API

   cmd.show( string representation="", string selection="" )

EXAMPLES

   show lines,(name ca or name c or name n)
   show ribbon

NOTES

   "selection" can be an object name
   "show" alone will turn on lines for all bonds.

SEE ALSO

   hide, enable, disable


smooth

DESCRIPTION

   "smooth" performs a window average over a series of states.  This
   type of averaging is often used to suppress high-frequency vibrations
   in a molecular dynamics trajectory.

USAGE

   smooth [selection [, passes [,window [,first [,last [, ends]]]]]]

SEE ALSO

   load_traj

ARGUMENTS

   ends (0 or 1) controls whether or not the end states are also smoothed
   using a weighted asymmetric window

NOTES

   This function is not memory efficient.  For reasons of flexibility,
   it uses two additional copies of every atomic coordinate for the
   calculation.  If you are memory-constrained in visualizing MD
   trajectories, then you may want to use an external tool such as
   Amber's ptraj to perform smoothing before loading coordinates into
   PyMOL.


sort

DESCRIPTION

   "sort" reorders atoms in the structure.  It usually only necessary
   to run this routine after an "alter" command which has modified the
   names of atom properties.  Without an argument, sort will resort
   all atoms in all objects.

USAGE

   sort [object]

PYMOL API

   cmd.sort(string object)

SEE ALSO

   alter


space

DESCRIPTION

   "space" selects a color palette (or color space).
   
USAGE

   space space-name
   
PYMOL API
   cmd.space(string space_name)
   
EXAMPLES

   space rgb
   space cmyk
   space pymol


spectrum

DESCRIPTION

   "spectrum" colors atoms using a spectrum
   
USAGE

PYMOL API

EXAMPLES


spheroid

DESCRIPTION

   "spheroid" averages trajectory frames together to create
   an ellipsoid-like approximation of the actual anisotropic
   motion exhibited by the atom over a series of trajectory frames.

USAGE

   spheroid object,average

   average = number of states to average for each resulting spheroid state


splash

DESCRIPTION

   "splash" shows the splash screen information.

USAGE

   splash


split_states



stereo

DESCRIPTION

   "stereo" activates or deactives stereo mode.

USAGE

   stereo on
   stereo off
   stereo swap
   stereo crosseye
   stereo walleye
   stereo quadbuffer

NOTES

   quadbuffer is the default stereo mode if hardware stereo is available
   otherwise, crosseye is the default.

PYMOL API

   cmd.stereo(string state="on")


symexp

DESCRIPTION

   "symexp" creates all symmetry related objects for the specified object
   that occurs within a cutoff about an atom selection.  The new objects
   are labeled using the prefix provided along with their crystallographic
   symmetry operation and translation.

USAGE

   symexp prefix = object, (selection), cutoff

PYMOL API

   cmd.symexp( string prefix, string object, string selection, float cutoff) 

SEE ALSO

   load


sync

DESCRIPTION

   "sync" is an API-only function which waits until all current
   commmands have been executed before returning.  A timeout
   can be used to insure that this command eventually returns.

PYMOL API

   cmd.sync(float timeout=1.0,float poll=0.05)

SEE ALSO

   frame


system

DESCRIPTION

   "system" executes a command in a subshell under Unix or Windows.

USAGE

   system command 

PYMOL API

   cmd.system(string command,int sync=1)

NOTES

   async can only be specified from the Python level (not the command language)

   if async is 0 (default), then the result code from "system" is returned in r

   if async is 1, then the command is run in a separate thread whose object is
   returned

SEE ALSO

   ls, cd, pwd


torsion

DESCRIPTION

   "torsion" rotates the torsion on the bond currently
   picked for editing.  The rotated fragment will correspond
   to the first atom specified when picking the bond (or the
   nearest atom, if picked using the mouse).

USAGE

   torsion angle

PYMOL API

   cmd.torsion( float angle )

SEE ALSO

   edit, unpick, remove_picked, cycle_valence


transform_selection

"transform_selection" is currently UNSUPPORTED, but some information has
been provided via the mailing list:

RE: transform_selection

cmd.transform_selection(string selection, list-of-16-floats matrix, int state-number):

Note that matrix is NOT a standard homogenous 4x4 transformation
matrix.  Instead it is something PyMOL-specific which consists of the
following:

1) a 3x3 matrix containing the rotation in the upper-left quadrant

2) a 3x1 translation to be applied before rotation in the right-hand
   column (matrix[3],matrix[7],matrix[11])

3) a 1x3 translation to be applied after rotation in the bottom row
   (matrix[12],matrix[13],matrix[14]).

In other words, if the matrix is:

[  m0  m1  m2  m3
   m4  m5  m6  m7
   m8  m9 m10 m11
  m12 m13 m14 m15 ]

Atoms will be transformed as follows

Y = M X

y0 = m0*(x0+m3) + m4*(x1+m7) +  m8*(x2+m11) + m12
y1 = m1*(x0+m3) + m5*(x1+m7) +  m9*(x2+m11) + m13
y2 = m2*(x0+m3) + m6*(x1+m7) + m10*(x2+m11) + m14


translate

DESCRIPTION

   "translate" can be used to translate the atomic coordinates of a
   molecular object.  Behavior differs depending on whether or not the
   "object" parameter is specified.

   If object is None, then translate translates atomic coordinates
   according to the vector provided for the selection and in the state
   provided.  All representation geometries will need to be
   regenerated to reflect the new atomic coordinates.

   If object is set to an object name, then selection and state are
   ignored and instead of translating the atomic coordinates, the
   object's overall representation display matrix is modified.  This
   option is for use in animations only.

   The "camera" option controls whether the camera or the model's
   axes are used to interpret the translation vector.

USAGE

   translate vector [,selection [,state [,camera [,object ]]]]

PYMOL API

   cmd.translate(list vector, string selection = "all", int state = 0,
                 int camera = 1, string object = None)

EXAMPLES

   translate [1,0,0], name ca

NOTES

   if state = 0, then only visible state(s) are affected.
   if state = -1, then all states are affected.


turn

DESCRIPTION

   "turn" rotates the camera about one of the three primary axes,
   centered at the origin.

USAGE

   turn axis, angle

EXAMPLES

   turn x,90
   turn y,45

PYMOL API

   cmd.turn( string axis, float angle )

SEE ALSO

   move, rotate, translate, zoom, center, clip


unbond

DESCRIPTION

   "unbond" removes all bonds between two selections.

USAGE

   unbond atom1,atom2

PYMOL API

   cmd.unbond(selection atom1="(lb)",selection atom2="(rb)")

SEE ALSO

   bond, fuse, remove_picked, attach, detach, replace


undo

DESCRIPTION

   "undo" restores the previous conformation of the object currently
   being edited.

USAGE

   undo

SEE ALSO

   redo, push_undo


unmask

DESCRIPTION

   "unmask" reverses the effect of "mask" on the indicated atoms.

PYMOL API

   cmd.unmask( string selection="(all)" )

USAGE

   unmask (selection)

SEE ALSO

   mask, protect, deprotect, mouse


unpick

DESCRIPTION

   "unpick" deletes the special "pk" atom selections (pk1, pk2, etc.)
   used in atom picking and molecular editing.

USAGE

   unpick

PYMOL API

   cmd.unpick()

SEE ALSO

   edit


unset

DESCRIPTION

   "unset" behaves in two ways.

   If selection is not provided, unset changes the named global
   setting to a zero or off value.

   If a selection is provided, then "unset" undefines 
   object-specific or state-specific settings so that the global
   setting will be in effect.

USAGE

   unset name [,selection [,state ]]

PYMOL API

   cmd.unset ( string name, string selection = '',
            int state=0, int updates=1, int log=0 )


update

DESCRIPTION

   "update" transfers coordinates from one selection to another.
USAGE

   update (target-selection),(source-selection)

EXAMPLES

   update target,(variant)

NOTES

   Currently, this applies across all pairs of states.  Fine
   control will be added later.

SEE ALSO

   load


view

DESCRIPTION

   "view" makes it possible to save and restore viewpoints on a given
   scene within a single session.

USAGE

   view key[,action]
   view *

   key can be any string
   action should be 'store' or 'recall' (default: 'recall')

PYMOL API

   cmd.view(string key,string action)

VIEWS

   Views F1 through F12 are automatically bound to function keys
   provided that "set_key" hasn't been used to redefine the behaviour
   of the respective key, and that a "scene" hasn't been defined for
   that key.

EXAMPLES

   view 0,store
   view 0

SEE ALSO

   scene, set_view, get_view


viewport

DESCRIPTION

   "viewport" changes the size of the viewing port (and thus the size
   of all png files subsequently output)

USAGE

   viewport width, height

PYMOL API

   cmd.viewport(int width, int height)


wizard

DESCRIPTION

   "wizard" launches on of the built-in wizards.  There are special
   Python scripts which work with PyMOL in order to obtain direct user
   interaction and easily peform complicated tasks.

USAGE

   wizard name

PYMOL API

   cmd.wizard(string name)

EXAMPLE

   wizard distance  # launches the distance measurement wizard


zoom

DESCRIPTION

   "zoom" scales and translates the window and the origin to cover the
   atom selection.


USAGE

   zoom [ selection [,buffer [, state [, complete ]]]]

EXAMPLES

   zoom
   zoom complete=1
   zoom (chain A)
   zoom 142/

PYMOL API

   cmd.zoom( string selection, float buffer=0.0,
             int state=0, int complete=0 )

NOTES

   state = 0 (default) use all coordinate states
   state = -1 use only coordinates for the current state
   state > 0  use coordinates for a specific state

   complete = 0 or 1:
      Normally the zoom command tries to guess an optimal zoom level
   for visualization, balancing closeness against occasional clipping
   of atoms out of the field of view.  You can change this behavior by
   setting the complete option to 1, which will guarantee that the
   atom positions for the entire selection will fit in the field of an
   orthoscopic view.  To absolutely prevent clipping, you may also
   need to add a buffer (typically 2 A) to account for the perpective
   transformation and for graphical representations which extend
   beyond the atom coordinates..

SEE ALSO

   origin, orient, center


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