Document Sample
PymolRef Powered By Docstoc
					Pymol Reference Card                                         Basic Commands                                                  Image Output
                                                             Some commands used with atoms selections. If you are            low resolution                                     ray
Modes                                                        unsure about the selection, click on the molecule part that     high resolution                          ray 2000,2000
Pymol supports two modes of input: point and click mode,     you want in the viewing window and then look at the out-        ultra-high resolution                    ray 5000,5000
and command line mode. The point and click allows you to     put line to see the selection.                                  change the default size [pts]        viewport 640,480
quickly rotate the molecule(s) zoom in and out and change                                                                    image shadow control                  set ray shadow,0
                                                             fill viewer with selection                  zoom /pept//a
the clipping planes. The command line mode where com-                                                                        image fog control                  set ray trace fog,0
                                                             center a selection                       center /pept//a
mands are entered into the external GUI window supports                                                                      image depth cue control                set depth cue,0
                                                             colour a selection                 colour pink, /pept//a
all of the commands in the point and click mode, but is                                                                      image antialiasing control             set antialias,1
                                                             force Pymol to reapply colours                   recolor
more flexible and possibly useful for complex selection and                                                                   export image as .png                     png image.png
                                                             set background colour                     bg color white
command issuing. Commands entered on the command             vdW representation of selection show spheres, 156/ca            Hydrogen Bonding
line are executed when you press the return key.             stick representation of selection       show sticks, a//        Draw bonds between atoms and label the residues that are
command help                                help keyword     line representation of selection       show lines, /pept        involved.
                                                             ribbon representation of selection    show ribbon, /pept
Loading Files                                                dot representation of selection         show dots, /pept        draw a line between atoms      distance 542/oe1,538/ne
file loading                    load data/test/pept.pdb                                                                       set the line dash gap                  set dash gap,0.09
                                                             mesh representation of selection        show mesh, /pept
loading from terminal         pymol data/test/pept.pdb                                                                       set the line dash width               set dash width,3.0
                                                             surface representation of selection show surface, /pept
toggle between text and graphics                   Esc                                                                       set the line dash radius            set dash radius,0.0
                                                             nonbonded representation of selection show nonbonded,
toggle Y axis rocking                             rock                                                                       set the line dash length           set dash length,0.15
stereo view                              stereo on/off                                                                       set round dash ends              set dash round ends,on
                                                             nonbonded sphere representation of selection        show
stereo type stereo crosseye / walleye / quadbuffer                                                                           hide a label                        hide labels, dist01
                                                             nb spheres, /pept
undo action                                       undo                                                                       label a reside         label (542/oe1), "%s" %("E542")
                                                             cartoon representation of selection    show cartoon, a//
reset view                                       reset                                                                       set label font                       set label font id,4
                                                             clear all                                       hide all
reinitialize Pymol                        reinitialize                                                                       set label colour                  set label color,white
                                                             rotate a selection       rotate axis, angle, selection
quit (force, even if unsaved)                     quit
                                                             translate a selection     translate [x,y,z], selection          Electrostatics
Mouse Control                                                Cartoon Settings                                                There are a number of ways to apply electrostatics in Py-
                                                                                                                             mol. The user can use GRASP to generate a map and then
                                                             Setting the value at the end to 0 forces the secondary struc-
              L        M      R      Wheel                                                                                   import it. Alternatively the user can use the APBS Pymol
                                                             ture to go though the CA position.
            Rota     Move    MovZ    Slab                                                                                    plugin. Pymol also has a built in function that is quick
                                                             cylindrical helices set cartoon cylindrical helices,1
  Shift     +Box -Box        Clip    MovS                                                                                    and dirty.
                                                             fancy helices [tubular edge]                             set
  Ctrl       +/-     PkAt    Pk1      —                                                                                      generate electrostatic surface action > generate>vacuum
                                                             cartoon fancy helices,1
  CtSh       Sele     Cent   Menu     —                                                                                      electrostatics > protein contact potential
                                                             flat sheets                     set cartoon flat sheets,1
  DblClk Menu Cent           PkAt     —                      smooth loops                  set cartoon smooth loops,1        Pymol Movies (mac)
set the center of rotation            origin selection       find rings for cartoon                                    set    move the camera                              move x,10
                                                             cartoon ring finder,[1,2,3,4]                                   turn the camera                              turn x,90
Atom Selection                                               ring mode                 set cartoon ring mode,[1,2,3]
object-name/segi-id/chain-id/resi-id/name-id                                                                                 play the movie                                   mplay
                                                             nucleic acid mode set nucleic acid mode,[0,1,2,3,4]             stop the movie                                   mstop
molecular system selection                      /pept        cartoon sidechains       set cartoon side chain helper;         writeout png files      mpng prefix [, first [, last]]
molecule selection                          /pept/lig        rebuild                                                         show a particular frame                  frame number
chain selection                           /pept/lig/a        primary colour                     set cartoon color,blue       move forward on frame                          forward
residue selection                      /pept/lig/a/10        secondary colour      set cartoon highlight color,grey          move back one frame                          backwards
atom                                /pept/lig/a/10/ca        limit colour to ss       set cartoon discrete colors,on         go to the start of the movie                    rewind
ranges                                 lig/a/10-12/ca        cartoon transparency       set cartoon transparency,0.5         go to the middle of the movie                   middle
ranges                                      a/6+8/c+o        cartoon loop                             cartoon loop, a//      go to the movie end                             ending
missing selections                           /pept//a        cartoon loop                             cartoon loop, a//      determine the current frame                  get frame
naming a selection           select bb, name c+o+n+ca        cartoon rectangular                      cartoon rect, a//      clear the movie cache                           mclear
count atoms in a selection             count atoms bb        cartoon oval                             cartoon oval, a//      execute a command in a frame mdo 1, turn x,5; turn
remove atoms from a selection           remove resi 5        cartoon tubular                          cartoon tube, a//      y,5;
general all, none, hydro, hetatm, visible, present           cartoon arrow                          cartoon arrow, a//       dump current movie commands                      mdump
atoms not in a selection     select sidechains, ! bb         cartoon dumbell                      cartoon dumbell, a//       reset the number of frames per second      meter reset
atoms with a vdW gap < 3 ˚  A         resi 6 around 3        b-factor sausage                       cartoon putty, a//
atom centers with a gap < 1.0 ˚ all near 1 of resi 6
atom centers within < 4.0 ˚A   all within 4 of resi 6
Miscellaneous                                              Secondary Structures                                         NMR Structures
add hydrogens in to a molecule selection           h add   Pymol has a secondary structure determination algorithm      NMR models should be loaded into the same object, but
alias a set of commands separated by ”;” alias go,load     called dss, however it is better to use the DSSP algorithm   should have different states. load a model into an object
1hpv.pdb; zoom 200/; show sticks, 200/ around 8            and then define the limits manually.                          load file.pdb, object
structurally align            align prot1////CA, prot2,                                                                 show all models in an object           set all states,1
                                                           to run dss                                 dss selection
object=alignment                                                                                                        show only one object model             set all states,0
                                                           to define helical structure          alter 11-40/, ss=’H’
fit one molelcule to another       fit selection, target                                                                 show a particular model             frame model number
                                                           to define loop regions               alter 40-50/, ss=’L’
copy at selection                   copy target, source                                                                 determine which model                         get model
                                                           to define strand structure           alter 50-60/, ss=’S’
create a new selection         create target, selection                                                                 fit two structures to one another         fit selection
                                                           rebuild the cartoon after alteration             rebuild
delete a selection                     delete selection                                                                 fit and calculate the rms                 rms selection
                                                           get dihedral angle      get dihedral 4/n,4/c,4/ca,4/cb
save file                       save filename, selection                                                                 rms without fitting                   rms cur selection
protect or deprotect a selection [de]protect selection                                                                  fit ensemble structures           intra fit selection,1
mask or demask to allow/stop selection         [un]mask    Files                                                        calculate rms                intra rms selection,state
selection                                                  change the working directory                  cd <path>      ensemble rms without fitting               intra rms cur
align coordinates with axis            orient selection    list contents of current directory                    ls     selection,state
get the current rotation matrix                 get view   print current working directory                      pwd
input a rotation matrix                         set view                                                                Changing Structures
safely refresh the scene                         refresh   Crystal Structures                                           add a bond                          bond atom1, atom2
store a scene            view name, store, description                                                        ˚
                                                           To recreate crystal packing of molelcules within 5 A of      remove bonds                       unbond atom1,atom2
restore a view                      view name, [recall]    pept in the pept.pdb (which must contain CRYST date),        join to molecules together        fuse [atom1, atom2]
set a new colour                    set color name, rgb    use the symexp command.                          symexp
                                                           sym,pept,(pept),5.0                                          Old School Images
                                                                                                                        Load a .pdb and make a cartoon view. Then change the
                                                                                                                        background colour to white and change the ray mode to 2.
                                                                                                                                                          set ray trace mode,2
                                                                                                                        make the lines thinner                 set antialias,2
                                                                                                                        raytrace the image                                  ray

c 2007-2009 R. Bryn Fenwick – licensed under the terms of the GNU General Public License 2.0 or later.