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|
PyMOL>reinit
PyMOL>set matrix_mode, 0
Setting: matrix_mode set to 0.
PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>remove not resi 5
Remove: eliminated 97 atoms in model "pept".
PyMOL>iterate_state 1,all,print "%8.3f %8.3f %8.3f"%(x,y,z)
-0.135 -5.634 21.235
-0.006 -4.205 21.043
-1.408 -3.636 20.918
-2.092 -3.870 19.914
0.791 -3.871 19.783
0.939 -2.396 19.549
0.582 -1.619 18.499
1.470 -1.542 20.495
1.431 -0.303 20.038
0.896 -0.322 18.831
IterateState: iterated over 10 atom coordinate states.
PyMOL>rotate x, 53, object=pept
PyMOL>rotate y, 27, object=pept
PyMOL>rotate z, 6, object=pept
PyMOL>translate [1,2,3], object=pept
PyMOL>save tmp/C1110a.pdb
Save: wrote "tmp/C1110a.pdb".
PyMOL>for a in open("tmp/C1110a.pdb").readlines(): print a,
ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N
ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C
ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C
ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O
ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C
ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N
END
PyMOL>save tmp/C1110b.pdb, ref=pept
Save: wrote "tmp/C1110b.pdb".
PyMOL>for a in open("tmp/C1110b.pdb").readlines(): print a,
ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N
ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C
ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C
ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O
ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C
ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N
END
PyMOL>load dat/pept.pdb, tmp
CmdLoad: "dat/pept.pdb" loaded as "tmp".
PyMOL>remove tmp and not resi 5
Remove: eliminated 97 atoms in model "tmp".
PyMOL>matrix_transfer pept, tmp
PyMOL>save tmp/C1110c.pdb, tmp,
Save: wrote "tmp/C1110c.pdb".
PyMOL>for a in open("tmp/C1110c.pdb").readlines(): print a,
ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N
ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C
ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C
ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O
ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C
ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N
END
PyMOL>save tmp/C1110d.pdb, tmp, ref=tmp
Save: wrote "tmp/C1110d.pdb".
PyMOL>for a in open("tmp/C1110d.pdb").readlines(): print a,
ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N
ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C
ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C
ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O
ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C
ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N
END
PyMOL>reinit
PyMOL>set matrix_mode, 1
Setting: matrix_mode set to 1.
PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>remove not resi 5
Remove: eliminated 97 atoms in model "pept".
PyMOL>iterate_state 1,all,print "%8.3f %8.3f %8.3f"%(x,y,z)
-0.135 -5.634 21.235
-0.006 -4.205 21.043
-1.408 -3.636 20.918
-2.092 -3.870 19.914
0.791 -3.871 19.783
0.939 -2.396 19.549
0.582 -1.619 18.499
1.470 -1.542 20.495
1.431 -0.303 20.038
0.896 -0.322 18.831
IterateState: iterated over 10 atom coordinate states.
PyMOL>rotate x, 53, object=pept
PyMOL>rotate y, 27, object=pept
PyMOL>rotate z, 6, object=pept
PyMOL>translate [1,2,3], object=pept
PyMOL>save tmp/C1110a.pdb
Save: wrote "tmp/C1110a.pdb".
PyMOL>for a in open("tmp/C1110a.pdb").readlines(): print a,
ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N
ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C
ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C
ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O
ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C
ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N
END
PyMOL>save tmp/C1110b.pdb, ref=pept
Save: wrote "tmp/C1110b.pdb".
PyMOL>for a in open("tmp/C1110b.pdb").readlines(): print a,
ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N
ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C
ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C
ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O
ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C
ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N
END
PyMOL>load dat/pept.pdb, tmp
CmdLoad: "dat/pept.pdb" loaded as "tmp".
PyMOL>remove tmp and not resi 5
Remove: eliminated 97 atoms in model "tmp".
PyMOL>matrix_transfer pept, tmp
PyMOL>save tmp/C1110c.pdb, tmp,
Save: wrote "tmp/C1110c.pdb".
PyMOL>for a in open("tmp/C1110c.pdb").readlines(): print a,
ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N
ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C
ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C
ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O
ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C
ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N
END
PyMOL>save tmp/C1110d.pdb, tmp, ref=tmp
Save: wrote "tmp/C1110d.pdb".
PyMOL>for a in open("tmp/C1110d.pdb").readlines(): print a,
ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N
ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C
ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C
ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O
ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C
ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N
END
PyMOL>reinit
PyMOL>set matrix_mode, 2
Setting: matrix_mode set to 2.
PyMOL>load dat/pept.pdb
CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>remove not resi 5
Remove: eliminated 97 atoms in model "pept".
PyMOL>iterate_state 1,all,print "%8.3f %8.3f %8.3f"%(x,y,z)
-0.135 -5.634 21.235
-0.006 -4.205 21.043
-1.408 -3.636 20.918
-2.092 -3.870 19.914
0.791 -3.871 19.783
0.939 -2.396 19.549
0.582 -1.619 18.499
1.470 -1.542 20.495
1.431 -0.303 20.038
0.896 -0.322 18.831
IterateState: iterated over 10 atom coordinate states.
PyMOL>rotate x, 53, object=pept, object_mode=1
PyMOL>rotate y, 27, object=pept, object_mode=1
PyMOL>rotate z, 6, object=pept, object_mode=1
PyMOL>translate [1,2,3], object=pept, object_mode=1
PyMOL>save tmp/C1110a.pdb
Save: wrote "tmp/C1110a.pdb".
PyMOL>for a in open("tmp/C1110a.pdb").readlines(): print a,
ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N
ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C
ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C
ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O
ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C
ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N
END
PyMOL>save tmp/C1110b.pdb, ref=pept
Save: wrote "tmp/C1110b.pdb".
PyMOL>for a in open("tmp/C1110b.pdb").readlines(): print a,
ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N
ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C
ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C
ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O
ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C
ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N
END
PyMOL>load dat/pept.pdb, tmp
CmdLoad: "dat/pept.pdb" loaded as "tmp".
PyMOL>remove tmp and not resi 5
Remove: eliminated 97 atoms in model "tmp".
PyMOL>matrix_transfer pept, tmp
PyMOL>save tmp/C1110c.pdb, tmp,
Save: wrote "tmp/C1110c.pdb".
PyMOL>for a in open("tmp/C1110c.pdb").readlines(): print a,
ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N
ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C
ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C
ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O
ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C
ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N
END
PyMOL>save tmp/C1110d.pdb, tmp, ref=tmp
Save: wrote "tmp/C1110d.pdb".
PyMOL>for a in open("tmp/C1110d.pdb").readlines(): print a,
ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N
ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C
ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C
ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O
ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C
ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C
ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C
ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N
ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C
ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N
END
PyMOL>print "END-LOG"
|
