PyMOL>dele all
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>alter (elem n,o),vdw=4.0
 Alter: modified 36 atoms.
PyMOL>show dots
PyMOL>ray
 RayRenderTest: obtained 2032 graphics primitives.
PyMOL>alter_state 1,(all),x=x+y
 AlterState: modified 107 atom coordinate states.
PyMOL>hide
PyMOL>show lines
PyMOL>ray
 RayRenderTest: obtained 166 graphics primitives.
PyMOL>dele all
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" appended into object "pept", state 2.
PyMOL>alter_state -1,(all),x=x+y
 AlterState: modified 107 atom coordinate states.
PyMOL>alter_state 0,(all), x=x+y
 AlterState: modified 214 atom coordinate states.
PyMOL>alter_state 1,(all), x=x+y
 AlterState: modified 107 atom coordinate states.
PyMOL>alter_state 2,(all), x=x+y
 AlterState: modified 107 atom coordinate states.
PyMOL>alter_state 3,(all), x=x+y
 AlterState: modified 0 atom coordinate states.
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>remove hydro
 Remove: eliminated 20 atoms in model "small01".
PyMOL>h_add
PyMOL>count_atoms
 count_atoms: 36 atoms
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>remove id 17
 Remove: eliminated 1 atoms in model "small01".
PyMOL>count_atoms
 count_atoms: 35 atoms
PyMOL>edit id 3
 Selector: selection "pk1" defined with 1 atoms.
PyMOL>attach X,4,2
PyMOL>count_atoms
 count_atoms: 36 atoms
PyMOL>edit elem X
 Selector: selection "pk1" defined with 1 atoms.
PyMOL>remove_picked
 Remove: eliminated 1 atoms in model "small01".
PyMOL>unpick
PyMOL>print cmd.get_names()
['small01']
PyMOL>count_atoms
 count_atoms: 35 atoms
PyMOL>h_add
PyMOL>count_atoms
 count_atoms: 36 atoms
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>unbond id 1,id 2
 Unbond: 1 bonds removed from model "small01".
PyMOL>h_add
PyMOL>count_atoms
 count_atoms: 38 atoms
PyMOL>remove hydro
 Remove: eliminated 22 atoms in model "small01".
PyMOL>bond id 1,id 2
 Bond: 1 bonds added to model "small01".
PyMOL>h_add
PyMOL>count_atoms
 count_atoms: 36 atoms
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>edit id 6,id 10
 Selector: selection "pk1" defined with 1 atoms.
 Selector: selection "pk2" defined with 1 atoms.
PyMOL>cycle_valence
 Remove: eliminated 2 atoms in model "small01".
 Remove: eliminated 2 atoms in model "small01".
PyMOL>count_atoms
 count_atoms: 34 atoms
PyMOL>cycle_valence
 Remove: eliminated 1 atoms in model "small01".
 Remove: eliminated 1 atoms in model "small01".
PyMOL>count_atoms
 count_atoms: 32 atoms
PyMOL>remove_picked
PyMOL>bond id 6,id 10,2
 Bond: 1 bonds added to model "small01".
PyMOL>h_add
PyMOL>set valence=0.05
 Setting: valence set to on.
PyMOL>ray
 RayRenderTest: obtained 59 graphics primitives.
PyMOL>dele all
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -20.331,  13.157]
 cmd.extent: max: [   8.919,   0.863,  27.058]
PyMOL>protect resi 1-6
 Protect: 51 atoms protected from movement.
PyMOL>edit 2/sg,12/sg
 Selector: selection "pk1" defined with 1 atoms.
 Selector: selection "pk2" defined with 1 atoms.
PyMOL>torsion 90
PyMOL>get_extent
 cmd.extent: min: [ -10.445, -22.170,  11.965]
 cmd.extent: max: [   6.787,   0.863,  27.058]
PyMOL>undo
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -20.331,  13.157]
 cmd.extent: max: [   8.919,   0.863,  27.058]
PyMOL>redo
PyMOL>get_extent
 cmd.extent: min: [ -10.445, -22.170,  11.965]
 cmd.extent: max: [   6.787,   0.863,  27.058]
PyMOL>undo
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -20.331,  13.157]
 cmd.extent: max: [   8.919,   0.863,  27.058]
PyMOL>deprotect
 Protect: 107 atoms deprotected.
PyMOL>edit 2/sg,12/sg
 Selector: selection "pk1" defined with 1 atoms.
 Selector: selection "pk2" defined with 1 atoms.
PyMOL>torsion 90
PyMOL>get_extent
 cmd.extent: min: [ -15.562, -22.170,  11.965]
 cmd.extent: max: [   5.893,  -8.073,  25.808]
PyMOL>dele all
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>flag ignore,(!*/ca,c,n,o,cb)
 Flag: flag 25 is set in 43 of 107 atoms.
PyMOL>flag exfoliate,(*/cb)
 Flag: flag 24 is set in 12 of 107 atoms.
PyMOL>show surf
PyMOL>ray
 RepSurface: 921 surface points.
 RepSurface: 1838 triangles.
 RayRenderTest: obtained 1529 graphics primitives.
PyMOL>dele all
PyMOL>load dat/small01.mol,m1
 ExecutiveLoad: "dat/small01.mol" loaded as "m1", through state 1.
PyMOL>load dat/small01.mol,m2
 ExecutiveLoad: "dat/small01.mol" loaded as "m2", through state 1.
PyMOL>fuse m1 and id 31,m2 and id 31
PyMOL>dele m1
PyMOL>zoom
PyMOL>ray
 RayRenderTest: obtained 144 graphics primitives.
PyMOL>dele all
PyMOL>load dat/small01.mol,m1
 ExecutiveLoad: "dat/small01.mol" loaded as "m1", through state 1.
PyMOL>load dat/small01.mol,m2
 ExecutiveLoad: "dat/small01.mol" loaded as "m2", through state 1.
PyMOL>remove id 30
 Remove: eliminated 1 atoms in model "m1".
 Remove: eliminated 1 atoms in model "m2".
PyMOL>fuse m1 and id 12,m2 and id 12
PyMOL>dele m1
PyMOL>zoom
PyMOL>ray
 RayRenderTest: obtained 144 graphics primitives.
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>edit id 2,id 6, id 5
 Selector: selection "pk1" defined with 1 atoms.
 Selector: selection "pk2" defined with 1 atoms.
 Selector: selection "pk3" defined with 1 atoms.
PyMOL>invert
 Editor: Inverted atom.
PyMOL>print "%8.3f"%cmd.dist("id 28","id 17")
   1.957
PyMOL>dele all
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>iterate (name n),print resi
1
2
3
4
5
6
7
8
9
10
11
12
13
 Iterate: iterated over 13 atoms.
PyMOL>iterate_state 1,(name o),print "%8.3f %8.3f %8.3f"%(x,y,z)
   4.456  -15.889   23.517
   3.025  -12.039   25.188
   1.332   -9.867   21.362
   0.752   -5.592   23.297
  -2.092   -3.870   19.914
  -5.181   -3.100   20.933
  -5.188   -7.669   21.049
  -1.643   -7.529   19.691
  -0.699   -9.660   16.692
   2.708  -11.019   16.296
   3.449  -13.097   20.534
   5.278  -17.322   18.998
   5.962  -19.432   22.570
 IterateState: iterated over 13 atom coordinate states.
PyMOL>dele all
PyMOL>load dat/il2.pdb
 CmdLoad: "dat/il2.pdb" loaded as "il2".
PyMOL>stored.sum = 0
PyMOL>iterate_state 1,(il2),stored.sum=stored.sum+x
 IterateState: iterated over 2084 atom coordinate states.
PyMOL>print "%8.3f"%stored.sum
20809.421
PyMOL>push_undo (il2)
PyMOL>alter_state 1,(il2),x=0.0
 AlterState: modified 2084 atom coordinate states.
PyMOL>rebuild
PyMOL>stored.sum = 0
PyMOL>iterate_state 1,(il2),stored.sum=stored.sum+x
 IterateState: iterated over 2084 atom coordinate states.
PyMOL>print "%8.3f"%stored.sum
   0.000
PyMOL>edit il2`1
 Selector: selection "pk1" defined with 1 atoms.
PyMOL>undo
PyMOL>stored.sum = 0
PyMOL>iterate_state 1,(il2),stored.sum=stored.sum+x
 IterateState: iterated over 2084 atom coordinate states.
PyMOL>print "%8.3f"%stored.sum
20809.421
PyMOL>rebuild
PyMOL>show dots
PyMOL>ray
 RayRenderTest: obtained 111433 graphics primitives.
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>iterate (all),print name
C
C
C
C
C
C
C
C
C
C
C
C
C
C
O
O
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
 Iterate: iterated over 36 atoms.
PyMOL>rename small01
 Rename: renamed 33 atoms.
PyMOL>iterate (all),print name
C01
C02
C03
C04
C05
C06
C07
C08
C09
C10
C11
C12
C13
C
O14
O
H15
H16
H17
H18
H19
H20
H21
H22
H23
H24
H25
H26
H27
H28
H29
H30
H31
H32
H33
H
 Iterate: iterated over 36 atoms.
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>edit id 3
 Selector: selection "pk1" defined with 1 atoms.
PyMOL>replace N,3,3
 Remove: eliminated 1 atoms in model "small01".
PyMOL>dele all
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -20.331,  13.157]
 cmd.extent: max: [   8.919,   0.863,  27.058]
PyMOL>origin pept,object=pept
PyMOL>rotate x,-45,object=pept
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -18.391,  12.126]
 cmd.extent: max: [   8.919,  -1.236,  29.153]
PyMOL>reset
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -18.391,  12.126]
 cmd.extent: max: [   8.919,  -1.236,  29.153]
PyMOL>rotate x,45,pept
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -20.331,  13.157]
 cmd.extent: max: [   8.919,   0.863,  27.058]
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.
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -20.331,  13.157]
 cmd.extent: max: [   8.919,   0.863,  27.058]
PyMOL>set_dihedral 1/n,1/ca,1/c,1/o,180
 SetDihedral: adjusted to 180.000
PyMOL>get_dihedral 1/n,1/ca,1/c,1/o
 cmd.get_dihedral: 180.000 degrees.
PyMOL>get_extent
 cmd.extent: min: [  -1.282, -17.809,   6.314]
 cmd.extent: max: [  10.270,  -4.939,  29.070]
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>remove not id 3
 Remove: eliminated 35 atoms in model "small01".
PyMOL>zoom
PyMOL>count_atoms
 count_atoms: 1 atoms
PyMOL>set_geometry (id 3),4,4
PyMOL>h_add
PyMOL>count_atoms
 count_atoms: 5 atoms
PyMOL>remove hydro
 Remove: eliminated 4 atoms in model "small01".
PyMOL>set_geometry (id 3),3,3
PyMOL>h_add
PyMOL>count_atoms
 count_atoms: 4 atoms
PyMOL>remove hydro
 Remove: eliminated 3 atoms in model "small01".
PyMOL>set_geometry (id 3),2,2
PyMOL>h_add
PyMOL>count_atoms
 count_atoms: 3 atoms
PyMOL>remove hydro
 Remove: eliminated 2 atoms in model "small01".
PyMOL>set_geometry (id 3),4,2
PyMOL>h_add
PyMOL>count_atoms
 count_atoms: 3 atoms
PyMOL>dele all
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>alter (all),resi = (999-int(resi)-ID/4)
 Alter: modified 107 atoms.
PyMOL>sort
PyMOL>show sph,(byres id 10)
PyMOL>ray
 RayRenderTest: obtained 210 graphics primitives.
PyMOL>dele all
PyMOL>dele all
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -20.331,  13.157]
 cmd.extent: max: [   8.919,   0.863,  27.058]
PyMOL>cmd.edit("(pept`95)",pkresi=1)
PyMOL>cmd.push_undo("pept",1)
PyMOL>cmd.edit("(pept`10)",pkresi=1)
PyMOL>cmd.push_undo("pept",1)
PyMOL>get_extent
 cmd.extent: min: [  -5.124, -31.391,  12.760]
 cmd.extent: max: [   8.919, -12.759,  27.469]
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>cmd.edit("(small01`3)",pkresi=1)
PyMOL>cmd.edit_mode()
PyMOL>cmd.push_undo("small01",1)
PyMOL>get_extent
 cmd.extent: min: [ -15.344,  -2.159,  -3.683]
 cmd.extent: max: [  -3.585,   2.683,   3.171]
PyMOL>undo
PyMOL>get_extent
 cmd.extent: min: [  -8.369,  -2.595,  -4.337]
 cmd.extent: max: [   2.256,   2.247,   2.517]
PyMOL>dele all
PyMOL>load dat/small01.mol
 ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.
PyMOL>get_extent
 cmd.extent: min: [  -8.369,  -2.595,  -4.337]
 cmd.extent: max: [   2.256,   2.247,   2.517]
PyMOL>cmd.set('valence','0.0500')
PyMOL>cmd.edit_mode()
PyMOL>cmd.push_undo("small01",1)
PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.120608196,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.040202755,   -0.160811022,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.120608196,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.040202755,   -0.160811022,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.160810933,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.160810933,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.120608196,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.020101367,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.160810933,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.160810933,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",   -0.020101367,    0.000000000,    0.000000000,1,1,0)
PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,    0.000000000,    0.000000000,1,1,0)
PyMOL>get_extent
 cmd.extent: min: [  -8.369,  -3.896,  -4.337]
 cmd.extent: max: [   2.256,   2.247,   2.517]
PyMOL>undo
PyMOL>get_extent
 cmd.extent: min: [  -8.369,  -2.595,  -4.337]
 cmd.extent: max: [   2.256,   2.247,   2.517]
PyMOL>dele all
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>get_extent
 cmd.extent: min: [  -5.188, -20.331,  13.157]
 cmd.extent: max: [   8.919,   0.863,  27.058]
PyMOL>load dat/pept.pdb,sav
 CmdLoad: "dat/pept.pdb" loaded as "sav".
PyMOL>alter_state 1,(pept),x=1;y=2;z=3;
 AlterState: modified 107 atom coordinate states.
PyMOL>rebuild
PyMOL>get_extent pept
 cmd.extent: min: [   1.000,   2.000,   3.000]
 cmd.extent: max: [   1.000,   2.000,   3.000]
PyMOL>update pept,sav
 Update: coordinates updated for 107 atoms.
PyMOL>get_extent pept
 cmd.extent: min: [  -5.188, -20.331,  13.157]
 cmd.extent: max: [   8.919,   0.863,  27.058]
