PyMOL contains an overwhelming number of commands, so we recommend that you first learn the core set of commands and then expand outward from there as your needs dictate.

A complete alphabetical list of commands is also available, and the concept of a command is also discussed.

See also: http://pymol.org/pymol-command-ref.html

load | save | order | group

color | set_color | bg_color | recolor | space | spectrum | ramp_new | draw | ray | png | mpng

set | unset | get | set_bond | unset_bond | reinitialize | full_screen | stereo | button | mouse | config_mouse | feedback

show | hide | color | label | spectrum | cartoon | scene | ramp_new

zoom | orient | origin | center | view | mview | scene | get_viewport

align | pair_fit | fit | rms | rms_cur | intra_fit | intra_rms | intra_rms_cur | matrix_copy | matrix_reset

distance | angle | dihedral

load | isodot | isomesh | isolevel | symexp | stereo

load | isodot | isomesh | isosurface | isolevel | map_new | slice_new | ramp_new | gradient

mset | madd | mdo | mappend | mview | frame | count_frames | count_states | forward | backward | rewind | middle | ending | mmatrix | mpng

@ | run | spawn | abort | skip | python | alias | embed | load_embedded

remove | rotate | translate | drag | set_dihedral | edit | torsion | cycle_valence | alter | alter_state | fragment | bond | attach | h_add | h_fill | h_fix | fix_chemistry | redo | undo

sculpt_activate | sculpt_deactivate | sculpt_iterate | sculpt_purge

multisave | dump | cls | splash | check