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PyMOL>dele all
PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>count_atoms
count_atoms: 107 atoms
PyMOL>count_atoms name ca
count_atoms: 13 atoms
PyMOL>count_states
cmd.count_states: 1 states.
PyMOL>create pept,(all),1,2
Selector: found 107 atoms.
PyMOL>create pept,(all),1,3
Selector: found 107 atoms.
PyMOL>create pept,(none),1,2
Selector: found 0 atoms.
PyMOL>create cpy,(all),1,1
Selector: found 107 atoms.
Executive: object "cpy" created.
PyMOL>count_states
cmd.count_states: 3 states.
PyMOL>count_states pept
cmd.count_states: 3 states.
PyMOL>count_states cpy
cmd.count_states: 1 states.
PyMOL>count_frames
cmd.count_frames: 3 frames
PyMOL>mset 1 x10
PyMOL>count_frames
cmd.count_frames: 10 frames
PyMOL>cmd.count_frames()
PyMOL>cmd.count_states()
PyMOL>cmd.count_atoms()
PyMOL>dist
cmd-Error: The 'pk1' selection is undefined.
cmd-Error: The 'pk2' selection is undefined.
PyMOL>distance
cmd-Error: The 'pk1' selection is undefined.
cmd-Error: The 'pk2' selection is undefined.
PyMOL>select lb,resi 5 and name ca
Selector: selection "lb" defined with 2 atoms.
PyMOL>dist
cmd-Error: The 'pk1' selection is undefined.
cmd-Error: The 'pk2' selection is undefined.
PyMOL>select rb,resi 8 and name ca
Selector: selection "rb" defined with 2 atoms.
PyMOL>dist
cmd-Error: The 'pk1' selection is undefined.
cmd-Error: The 'pk2' selection is undefined.
PyMOL>dist (lb),resi 10 and name ca
Executive: object "dist01" created.
PyMOL>distance resi 6 and name n,resi 9
Executive: object "dist02" created.
PyMOL>distance resi 7 and name ca,all,3.0,zoom=1
Executive: object "dist03" created.
PyMOL>print "%6.3f"%cmd.distance("resi 1 and name ca","resi 13 and name ca")
5.762
PyMOL>print "%6.3f"%cmd.distance("resi 1 and name ca","resi 14 and name ca")
-1.000
PyMOL>print cmd.find_pairs("name o","name n",mode=1,cutoff=3.4)
[(('cpy', 103), ('pept', 1)), (('pept', 103), ('pept', 1)), (('cpy', 83), ('pept', 15)), (('pept', 83), ('pept', 15)), (('cpy', 59), ('pept', 34)), (('pept', 59), ('pept', 34)), (('cpy', 47), ('pept', 56)), (('cpy', 37), ('pept', 56)), (('pept', 47), ('pept', 56)), (('pept', 37), ('pept', 56)), (('cpy', 18), ('pept', 73)), (('pept', 18), ('pept', 73)), (('cpy', 4), ('pept', 100)), (('pept', 4), ('pept', 100)), (('cpy', 103), ('cpy', 1)), (('pept', 103), ('cpy', 1)), (('cpy', 83), ('cpy', 15)), (('pept', 83), ('cpy', 15)), (('cpy', 59), ('cpy', 34)), (('pept', 59), ('cpy', 34)), (('cpy', 47), ('cpy', 56)), (('cpy', 37), ('cpy', 56)), (('pept', 47), ('cpy', 56)), (('pept', 37), ('cpy', 56)), (('cpy', 18), ('cpy', 73)), (('pept', 18), ('cpy', 73)), (('cpy', 4), ('cpy', 100)), (('pept', 4), ('cpy', 100))]
PyMOL>dele all
PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>get_area (none)
cmd.get_area: 0.000 Angstroms^2.
PyMOL>get_area
cmd.get_area: 1381.186 Angstroms^2.
PyMOL>get_area state=2
Area-Error: Invalid state.
PyMOL>get_area name ca
cmd.get_area: 112.133 Angstroms^2.
PyMOL>load dat/3al1.pdb
HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1
TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: D, L-ALPHA-1;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 2 symmetry operators.
CmdLoad: "dat/3al1.pdb" loaded as "3al1".
PyMOL>get_area
Area-Error: Selection must be within a single object.
PyMOL>dele all
PyMOL>print lst
[('white', 0), ('black', 1), ('blue', 2), ('green', 3), ('red', 4), ('cyan', 5), ('yellow', 6), ('dash', 7), ('magenta', 8), ('salmon', 9)]
PyMOL>print cmd.get_color_tuple("red")
(1.0, 0.0, 0.0)
PyMOL>print cmd.get_color_tuple("blue")
(0.0, 0.0, 1.0)
PyMOL>print cmd.get_color_tuple("green")
(0.0, 1.0, 0.0)
PyMOL>print cmd.get_color_tuple("white")
(1.0, 1.0, 1.0)
PyMOL>dele all
PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>get_dihedral 1/n,1/ca,1/c,1/o
cmd.get_dihedral: -8.586 degrees.
-5.188 -20.331 13.157 8.919 0.863 27.058
-5.063 -17.973 17.858 7.053 -2.295 25.698
PyMOL>print len(cmd.get_model().atom)
107
PyMOL>print len(cmd.get_model("resi 1").bond)
7
PyMOL>dele all
PyMOL>print cmd.get_names()
[]
PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>print cmd.get_names()
['pept']
PyMOL>edit 4/ca
Selector: selection "pk1" defined with 1 atoms.
PyMOL>print cmd.get_names("all")
['pept', 'pk1', '_pkbase1', '_pkfrag1', '_pkbase2', '_pkfrag2', 'pkmol']
PyMOL>print cmd.get_names("selections")
['pk1', '_pkbase1', '_pkfrag1', '_pkbase2', '_pkfrag2', 'pkmol']
PyMOL>print cmd.get_names("objects")
['pept']
PyMOL>print cmd.get_names_of_type("object:molecule")
['pept']
PyMOL>print cmd.get_names_of_type("object:map")
[]
PyMOL>kee = pp.keys()[0]
PyMOL>print kee
('pept', 10)
PyMOL>cmd._dump_floats(pp[kee])
-124.163 170.604
PyMOL>reset
PyMOL>get_position
cmd.get_position: [ 1.224, -10.279, 20.545]
PyMOL>zoom resi 10
PyMOL>get_position
cmd.get_position: [ 2.395, -9.290, 18.016]
PyMOL>get_type
Parsing-Error: missing required argument: name
PyMOL>get_type nonexistent
cmd-Error: unrecognized name.
PyMOL>get_type pept
object:molecule
PyMOL>id_atom none
cmd-Error: atom none not found by id_atom.
PyMOL>id_atom all
cmd-Error: multiple atoms all found by id_atom.
PyMOL>id_atom 5/ca
cmd.id_atom: (id 35)
PyMOL>identify name ca
cmd.identify: (id 2)
cmd.identify: (id 10)
cmd.identify: (id 16)
cmd.identify: (id 21)
cmd.identify: (id 35)
cmd.identify: (id 45)
cmd.identify: (id 53)
cmd.identify: (id 57)
cmd.identify: (id 66)
cmd.identify: (id 74)
cmd.identify: (id 81)
cmd.identify: (id 95)
cmd.identify: (id 101)
PyMOL>index name ca
cmd.index: (pept`2)
cmd.index: (pept`10)
cmd.index: (pept`16)
cmd.index: (pept`21)
cmd.index: (pept`35)
cmd.index: (pept`45)
cmd.index: (pept`53)
cmd.index: (pept`57)
cmd.index: (pept`66)
cmd.index: (pept`74)
cmd.index: (pept`81)
cmd.index: (pept`95)
cmd.index: (pept`101)
PyMOL>overlap pept,pept
cmd.overlap: 549.083 Angstroms.
PyMOL>alter (all),vdw=0.0
Alter: modified 107 atoms.
PyMOL>overlap pept,pept
cmd.overlap: 0.000 Angstroms.
PyMOL>alter (all),vdw=0.5
Alter: modified 107 atoms.
PyMOL>overlap pept,pept
cmd.overlap: 53.500 Angstroms.
PyMOL>phi_psi all
CYS-2: ( -124.2, 170.6 )
ALA-3: ( -128.4, 140.0 )
TRP-4: ( -128.5, 135.2 )
HIS-5: ( -114.1, 109.1 )
LEU-6: ( 53.9, 41.8 )
GLY-7: ( 90.4, -28.0 )
GLU-8: ( -75.5, 138.7 )
LEU-9: ( -73.5, 125.3 )
VAL-10: ( -91.9, -61.0 )
TRP-11: ( -168.2, 159.0 )
CYS-12: ( -138.9, 133.5 )
PyMOL>dele all
PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>get_symmetry
get_symmetry: No symmetry defined.
PyMOL>get_symmetry pept
get_symmetry: No symmetry defined.
PyMOL>get_symmetry none
Error: selection must refer to exactly one object.
PyMOL>load dat/3al1.pdb
HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1
TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: D, L-ALPHA-1;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 2 symmetry operators.
CmdLoad: "dat/3al1.pdb" loaded as "3al1".
PyMOL>get_symmetry
Error: selection must refer to exactly one object.
PyMOL>get_symmetry 3al1
get_symmetry: A = 20.544 B = 20.859 C = 26.055
get_symmetry: Alpha = 101.160 Beta = 97.030 Gamma = 118.060
get_symmetry: SpaceGroup = P -1
PyMOL>get_symmetry pept
get_symmetry: No symmetry defined.
PyMOL>hide
PyMOL>show cell,pept
PyMOL>ray renderer=2
RayRenderTest: obtained 0 graphics primitives.
PyMOL>apply(cmd.set_symmetry,["pept"]+cmd.get_symmetry("3al1"))
Symmetry: Found 2 symmetry operators.
PyMOL>get_symmetry pept
get_symmetry: A = 20.544 B = 20.859 C = 26.055
get_symmetry: Alpha = 101.160 Beta = 97.030 Gamma = 118.060
get_symmetry: SpaceGroup = P -1
PyMOL>get_symmetry 3al1
get_symmetry: A = 20.544 B = 20.859 C = 26.055
get_symmetry: Alpha = 101.160 Beta = 97.030 Gamma = 118.060
get_symmetry: SpaceGroup = P -1
PyMOL>show cell,pept
PyMOL>ray renderer=2
RayRenderTest: obtained 12 graphics primitives.
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