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PyMOL>load dat/pept.pdb, mol1
CmdLoad: "dat/pept.pdb" loaded as "mol1".
PyMOL>load dat/pept.pdb, mol2
CmdLoad: "dat/pept.pdb" loaded as "mol2".
PyMOL>load dat/pept.pdb, mol3
CmdLoad: "dat/pept.pdb" loaded as "mol3".
PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \
PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \
PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))
[ 0.00 0.00 0.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol1"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol2"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol3"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>translate [2,3,4], object=mol2, object_mode=1
PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \
PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \
PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))
[ 5.38 0.00 5.38 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol1"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol2"))
[ 1.00 0.00 0.00 2.00
0.00 1.00 0.00 3.00
0.00 0.00 1.00 4.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol3"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>matrix= cmd.get_object_matrix("mol2")
PyMOL>cmd.transform_object("mol3",matrix, homogenous=1)
PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \
PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \
PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))
[ 5.38 5.38 0.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol1"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol2"))
[ 1.00 0.00 0.00 2.00
0.00 1.00 0.00 3.00
0.00 0.00 1.00 4.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol3"))
[ 1.00 0.00 0.00 2.00
0.00 1.00 0.00 3.00
0.00 0.00 1.00 4.00
0.00 0.00 0.00 1.00 ]
PyMOL>dele mol3
PyMOL>load dat/pept.pdb,mol3
CmdLoad: "dat/pept.pdb" loaded as "mol3".
PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \
PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \
PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))
[ 5.38 0.00 5.38 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol1"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol2"))
[ 1.00 0.00 0.00 2.00
0.00 1.00 0.00 3.00
0.00 0.00 1.00 4.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol3"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>matrix_transfer mol1, mol3
PyMOL>dump_mat(cmd.get_object_matrix("mol1"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol2"))
[ 1.00 0.00 0.00 2.00
0.00 1.00 0.00 3.00
0.00 0.00 1.00 4.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol3"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \
PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \
PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))
[ 5.38 0.00 5.38 ]
PyMOL>matrix_transfer mol2, mol3
PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \
PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \
PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))
[ 5.38 5.38 0.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol1"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol2"))
[ 1.00 0.00 0.00 2.00
0.00 1.00 0.00 3.00
0.00 0.00 1.00 4.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("mol3"))
[ 1.00 0.00 0.00 2.00
0.00 1.00 0.00 3.00
0.00 0.00 1.00 4.00
0.00 0.00 0.00 1.00 ]
PyMOL>dele all
PyMOL>load ../data/tut/1hpv.pdb
HEADER HYDROLASE (ACID PROTEINASE) 18-NOV-94 1HPV 1HPV 2
COMPND HIV-1 PROTEASE (E.C.3.4.23.-) COMPLEXED WITH VX-478 1HPV 3
COMPND 2 (3(S)-N-(3-TETRAHYDROFURANYLOXYCARBONYL) AMINO-1- 1HPV 4
COMPND 3 (N,N-ISOBUTYL,4-AMINOBENZENESULFONYL) AMINO-2-(S)-HYDROXY- 1HPV 5
COMPND 4 4-PHENYLBUTANE) 1HPV 6
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 6 symmetry operators.
CmdLoad: "../data/tut/1hpv.pdb" loaded as "1hpv".
PyMOL>create ligand, organic
Selector: found 35 atoms.
Executive: object "ligand" created.
PyMOL>create protein, polymer
Selector: found 1516 atoms.
Executive: object "protein" created.
PyMOL>delete 1hpv
PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))
[ 6.86 5.47 8.86 ]
PyMOL>translate [2,3,4], object=protein, object_mode=1
PyMOL>rotate x, 20, object=protein, object_mode=1
PyMOL>rotate y, 40, object=protein, object_mode=1
PyMOL>rotate z, 90, object=protein, object_mode=1
PyMOL>translate [4,5,6], object=protein, object_mode=1
PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))
[ 22.69 18.69 18.07 ]
PyMOL>matrix_transfer protein, ligand
PyMOL>dump_mat(cmd.get_object_matrix("protein"))
[ 0.00 -0.94 0.34 30.89
0.77 0.22 0.60 11.28
-0.64 0.26 0.72 13.10
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("ligand"))
[ 0.00 -0.94 0.34 30.89
0.77 0.22 0.60 11.28
-0.64 0.26 0.72 13.10
0.00 0.00 0.00 1.00 ]
PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))
[ 6.86 5.47 8.86 ]
PyMOL>load ../data/tut/1hpv.pdb, copy
HEADER HYDROLASE (ACID PROTEINASE) 18-NOV-94 1HPV 1HPV 2
COMPND HIV-1 PROTEASE (E.C.3.4.23.-) COMPLEXED WITH VX-478 1HPV 3
COMPND 2 (3(S)-N-(3-TETRAHYDROFURANYLOXYCARBONYL) AMINO-1- 1HPV 4
COMPND 3 (N,N-ISOBUTYL,4-AMINOBENZENESULFONYL) AMINO-2-(S)-HYDROXY- 1HPV 5
COMPND 4 4-PHENYLBUTANE) 1HPV 6
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 6 symmetry operators.
CmdLoad: "../data/tut/1hpv.pdb" loaded as "copy".
PyMOL>create copy_ligand, copy and organic
Selector: found 35 atoms.
Executive: object "copy_ligand" created.
PyMOL>create copy_protein, copy and polymer
Selector: found 1516 atoms.
Executive: object "copy_protein" created.
PyMOL>create copy_protein2, copy and polymer
Selector: found 1516 atoms.
Executive: object "copy_protein2" created.
PyMOL>delete copy
PyMOL>matrix_transfer protein, copy_protein2
PyMOL>fit copy_protein, protein
Executive: RMS = 0.000 (1516 to 1516 atoms)
PyMOL>dump_mat(cmd.get_object_matrix("protein"))
[ 0.00 -0.94 0.34 30.89
0.77 0.22 0.60 11.28
-0.64 0.26 0.72 13.10
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("copy_protein"))
[ 0.00 -0.94 0.34 30.89
0.77 0.22 0.60 11.28
-0.64 0.26 0.72 13.10
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("copy_protein2"))
[ 0.00 -0.94 0.34 30.89
0.77 0.22 0.60 11.28
-0.64 0.26 0.72 13.10
0.00 0.00 0.00 1.00 ]
PyMOL>load ../data/tut/1hpv.pdb, target
HEADER HYDROLASE (ACID PROTEINASE) 18-NOV-94 1HPV 1HPV 2
COMPND HIV-1 PROTEASE (E.C.3.4.23.-) COMPLEXED WITH VX-478 1HPV 3
COMPND 2 (3(S)-N-(3-TETRAHYDROFURANYLOXYCARBONYL) AMINO-1- 1HPV 4
COMPND 3 (N,N-ISOBUTYL,4-AMINOBENZENESULFONYL) AMINO-2-(S)-HYDROXY- 1HPV 5
COMPND 4 4-PHENYLBUTANE) 1HPV 6
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 6 symmetry operators.
CmdLoad: "../data/tut/1hpv.pdb" loaded as "target".
PyMOL>dump_lst((cmd.get_distance("ligand////s1","/target/1HPV/B/ILE`84/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/target/1HPV/B/ILE`50/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /target/1HPV/B/VAL`82/CB")))
[ 14.32 17.77 18.33 ]
PyMOL>dump_mat(cmd.get_object_matrix("ligand"))
[ 0.00 -0.94 0.34 30.89
0.77 0.22 0.60 11.28
-0.64 0.26 0.72 13.10
0.00 0.00 0.00 1.00 ]
PyMOL>matrix_transfer target, ligand
PyMOL>dump_mat(cmd.get_object_matrix("ligand"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_lst((cmd.get_distance("ligand////s1","/target/1HPV/B/ILE`84/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/target/1HPV/B/ILE`50/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /target/1HPV/B/VAL`82/CB")))
[ 6.86 5.47 8.86 ]
PyMOL>dump_mat(cmd.get_object_matrix("protein"))
[ 0.00 -0.94 0.34 30.89
0.77 0.22 0.60 11.28
-0.64 0.26 0.72 13.10
0.00 0.00 0.00 1.00 ]
PyMOL>fit protein, target
Executive: RMS = 0.000 (1516 to 1516 atoms)
PyMOL>dump_mat(cmd.get_object_matrix("protein"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_mat(cmd.get_object_matrix("ligand"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))
[ 6.86 5.47 8.86 ]
PyMOL>matrix_transfer protein, ligand
PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \
PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))
[ 6.86 5.47 8.86 ]
PyMOL>dump_lst((cmd.get_distance("/target/1HPV/B/ILE`84/CB","/copy_protein2/1HPV/B/ILE`84/CB"),))
[ 19.55 ]
PyMOL>dump_mat(cmd.get_object_matrix("copy_protein2"))
[ 0.00 -0.94 0.34 30.89
0.77 0.22 0.60 11.28
-0.64 0.26 0.72 13.10
0.00 0.00 0.00 1.00 ]
PyMOL>matrix_reset copy_protein2
PyMOL>dump_mat(cmd.get_object_matrix("copy_protein2"))
[ 1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00 ]
PyMOL>dump_lst((cmd.get_distance("/target/1HPV/B/ILE`84/CB","/copy_protein2/1HPV/B/ILE`84/CB"),))
[ 0.00 ]
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