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PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>cls
PyMOL>print cmd.count_states()
1
PyMOL>print cmd.count_states("pept")
1
PyMOL>cmd.do("print 'it be done'")
PyMOL>print 'it be done'
it be done
PyMOL>viewport 200,150
PyMOL>stereo on
PyMOL>turn x,90
PyMOL>origin
PyMOL>origin (i;11)
PyMOL>origin pept
PyMOL>zoom (i;11)
PyMOL>zoom pept
PyMOL>zoom
PyMOL>frame 1
PyMOL>frame 2
PyMOL>move x,2
PyMOL>clip near,2
PyMOL>clip far,2
PyMOL>refresh
PyMOL>reset
PyMOL>meter_reset
PyMOL>mclear
PyMOL>mset 1 x10
PyMOL>mdo 1:turn x,5
PyMOL>mdo 2:turn y,10
PyMOL>rock
PyMOL>rock
PyMOL>forward
PyMOL>backward
PyMOL>rewind
PyMOL>ending
PyMOL>middle
PyMOL>mplay
PyMOL>mstop
PyMOL>color red
Executive: Colored 107 atoms.
PyMOL>color blue,(name n)
Executive: Colored 13 atoms.
PyMOL>flag 3=(resn his)
Flag: flag 3 is set in 10 of 107 atoms.
PyMOL>set_color dude = [ 1.0,0.6,0.3]
Color: "dude" defined as [ 1.000, 0.600, 0.300 ].
PyMOL>color dude,(name o)
Executive: Colored 13 atoms.
PyMOL>show sticks,(all)
PyMOL>hide
PyMOL>show lines
PyMOL>mmatrix store
PyMOL>turn x,45
PyMOL>mmatrix recall
PyMOL>disable
PyMOL>enable
PyMOL>mmatrix clear
PyMOL>refresh
PyMOL>rebuild
PyMOL>refresh
PyMOL>set line_smooth=1
Setting: line_smooth set to on.
PyMOL>label (all),chain
Label: labelled 107 atoms.
PyMOL>label (all),''
Label: labelled 107 atoms.
PyMOL>stored.cnt = 0
PyMOL>iterate (all),stored.cnt=stored.cnt+1
Iterate: iterated over 107 atoms.
PyMOL>print stored.cnt
107
PyMOL>stored.x = 0
PyMOL>iterate_state 1,(all),stored.x=stored.x+x
IterateState: iterated over 107 atom coordinate states.
PyMOL>print "%8.4f"%stored.x
130.9720
PyMOL>alter (all),segi='PEPT'
Alter: modified 107 atoms.
PyMOL>alter_state 1,(all),x = x + 1.0
AlterState: modified 107 atom coordinate states.
PyMOL>print "%8.4f"%cmd.get_dihedral("(i;11&n;n)","(i;11&n;ca)","(i;11&n;cb)","(i;11&n;cg)")
-160.7909
PyMOL>edit (i;11&n;n), (i;11&n;c), pkbond=0
Selector: selection "pk1" defined with 1 atoms.
Selector: selection "pk2" defined with 1 atoms.
PyMOL>dist
Executive: object "dist01" created.
PyMOL>dist (pk1),(pk2)
Executive: object "dist02" created.
PyMOL>dist tst
Executive: object "tst" created.
PyMOL>dist tst2 = (pk1),(pk2)
Executive: object "tst2" created.
PyMOL>bond
Bond: 1 bonds added to model "pept".
PyMOL>unbond
Unbond: 1 bonds removed from model "pept".
PyMOL>bond (pk1),(pk2),2
Bond: 1 bonds added to model "pept".
PyMOL>unbond (pk1),(pk2)
Unbond: 1 bonds removed from model "pept".
PyMOL>copy cpy=pept
Executive: object "cpy" created.
Executive: object cpy created.
PyMOL>select cpy_sel = (cpy)
Selector: selection "cpy_sel" defined with 107 atoms.
PyMOL>alter_state 1,(cpy),x=x+math.cos(y+z)
AlterState: modified 107 atom coordinate states.
PyMOL>rms cpy,pept
Executive: RMS = 0.695 (107 to 107 atoms)
PyMOL>rms (cpy and name ca),pept
Executive: RMS = 0.639 (13 to 13 atoms)
PyMOL>rms (cpy and name ca),(pept &n;ca)
Executive: RMS = 0.639 (13 to 13 atoms)
PyMOL>rms_cur cpy,pept
Executive: RMS = 0.700 (107 to 107 atoms)
PyMOL>rms_cur (cpy and name ca),pept
Executive: RMS = 0.722 (13 to 13 atoms)
PyMOL>rms_cur (cpy and name ca),(pept &n;ca)
Executive: RMS = 0.722 (13 to 13 atoms)
PyMOL>fit cpy,pept
Executive: RMS = 0.695 (107 to 107 atoms)
PyMOL>fit (cpy),(pept)
Executive: RMS = 0.695 (107 to 107 atoms)
PyMOL>fit (cpy and name ca),(pept &n;ca)
Executive: RMS = 0.639 (13 to 13 atoms)
PyMOL>pair_fit (cpy&i;11&n;ca),(pept&i;11&n;ca),\
PyMOL>(cpy&i;5&n;ca),(pept&i;5&n;ca),\
PyMOL>(cpy&i;1&n;ca),(pept&i;1&n;ca),\
PyMOL>(cpy&i;8&n;ca),(pept&i;8&n;ca)
ExecutiveRMS: RMS = 0.478 (4 to 4 atoms)
PyMOL>update (cpy),(pept)
Update: coordinates updated for 107 atoms.
PyMOL>remove (cpy and name c)
Remove: eliminated 13 atoms in model "cpy".
PyMOL>edit (cpy and i;11 & n;ca)
Selector: selection "pk1" defined with 1 atoms.
PyMOL>remove_picked
Remove: eliminated 1 atoms in model "cpy".
PyMOL>edit (cpy and i;5 & n;ca),(cpy and i;5 and n;cb)
Selector: selection "pk1" defined with 1 atoms.
Selector: selection "pk2" defined with 1 atoms.
PyMOL>alter (cpy),name=''
Alter: modified 93 atoms.
PyMOL>rename cpy
Rename: renamed 93 atoms.
PyMOL>rename cpy,1
Rename: renamed 93 atoms.
PyMOL>cycle_valence
PyMOL>cycle_valence
Remove: eliminated 1 atoms in model "cpy".
Remove: eliminated 1 atoms in model "cpy".
PyMOL>cycle_valence
PyMOL>remove_picked
PyMOL>edit (cpy and i;11 &n;n)
Editor-Error: Invalid input selection(s).
PyMOL>cmd.attach("H",1,1)
PyMOL>create tmp = (cpy&i;5)
Selector: found 13 atoms.
Executive: object "tmp" created.
PyMOL>fuse (cpy&i;11&n;cb),(tmp&n;cb)
PyMOL>edit (cpy and i;10 & n;n)
Editor-Error: Invalid input selection(s).
PyMOL>h_fill
PyMOL>h_fill
PyMOL>h_add (cpy)
PyMOL>edit (cpy and i;8 &n;o)
Editor-Error: Invalid input selection(s).
PyMOL>cmd.replace("S",3,1)
Error: you must first pick an atom to replace.
PyMOL>delete tmp
PyMOL>delete cpy
PyMOL>delete cpy_sel
PyMOL>edit (i;11&n;ca)
Selector: selection "pk1" defined with 1 atoms.
PyMOL>unpick
PyMOL>protect (pept and n;ca)
Protect: 13 atoms protected from movement.
PyMOL>protect pept
Protect: 107 atoms protected from movement.
PyMOL>protect
Protect: 107 atoms protected from movement.
PyMOL>deprotect (pept and n;ca)
Protect: 13 atoms deprotected.
PyMOL>deprotect
Protect: 107 atoms deprotected.
PyMOL>mask (pept and n;ca)
Mask: 13 atoms masked (cannot be picked or selected).
PyMOL>mask pept
Mask: 107 atoms masked (cannot be picked or selected).
PyMOL>mask
Mask: 107 atoms masked (cannot be picked or selected).
PyMOL>unmask (pept and n;ca)
Mask: 13 atoms unmasked.
PyMOL>unmask
Mask: 107 atoms unmasked.
PyMOL>edit (i;11&n;ca),(i;11&n;n),(i;11&n;c)
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>invert
Editor: Inverted atom.
PyMOL>edit (i;11&n;ca),(i;11&n;cb)
Selector: selection "pk1" defined with 1 atoms.
Selector: selection "pk2" defined with 1 atoms.
PyMOL>torsion 10
PyMOL>torsion -10
PyMOL>torsion 180
PyMOL>torsion 180
PyMOL>print cmd.get_model().__class__
chempy.models.Indexed
PyMOL>print "%8.3f"%cmd.get_area()
1381.186
PyMOL>print "%8.3f"%cmd.get_area("(name ca)")
112.133
PyMOL>print cmd.get_names()
['pept', 'dist01', 'dist02', 'tst', 'tst2']
PyMOL>print cmd.get_type('pept')
object:molecule
PyMOL>print cmd.identify("(i;7)")
[52, 53, 54, 55]
PyMOL>print "%8.4f %8.4f %8.4f %8.4f %8.4f %8.4f"%(ext[0][0],ext[0][1],ext[0][2],ext[1][0],ext[1][1],ext[1][2])
-4.1880 -20.3310 13.1570 9.9190 0.8630 27.0580
PyMOL>sort
PyMOL>sort pept
PyMOL>spheroid
Warning: 'spheroid' is experimental, incomplete, and unstable.
ObjectMolecule: computing spheroid from states 1 to 1.
PyMOL>spheroid pept
Warning: 'spheroid' is experimental, incomplete, and unstable.
ObjectMolecule: computing spheroid from states 1 to 1.
PyMOL>cmd.config_mouse(quiet=0)
config_mouse: three_button
PyMOL>rewind
PyMOL>dele all
PyMOL>load dat/ligs3d.sdf
ObjectMoleculeReadStr: read through molecule 1.
ObjectMoleculeReadStr: read through molecule 2.
ObjectMoleculeReadStr: read through molecule 3.
ObjectMoleculeReadStr: read through molecule 4.
ObjectMoleculeReadStr: read through molecule 5.
ObjectMoleculeReadStr: read through molecule 6.
ObjectMoleculeReadStr: read through molecule 7.
ObjectMoleculeReadStr: read through molecule 8.
ObjectMoleculeReadStr: read through molecule 9.
ObjectMoleculeReadStr: read through molecule 10.
ExecutiveLoad: "dat/ligs3d.sdf" loaded as "ligs3d", through state 10.
PyMOL>split_states ligs3d
PyMOL>print cmd.get_names()
['ligs3d', 'MFCD02681585', 'MFCD01567969', 'MFCD00023789', 'MFCD02579443', 'MFCD02579410', 'MFCD02579135', 'MFCD02681468', 'MFCD00141070', 'MFCD02983625', 'MFCD00115818']
PyMOL>rewind
PyMOL>ray renderer=2
RayRenderTest: obtained 564 graphics primitives.
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