
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms    5 (   25),  selected    5 , name T0335TS102_2
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS102_2.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      S       3           -
LGA    -       -      N       4           -
LGA    -       -      A       5           -
LGA    -       -      K       6           -
LGA    -       -      I       7           -
LGA    -       -      A       8           -
LGA    -       -      R       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    -       -      I      22           -
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    H      81      E      26          1.288
LGA    H      82      K      27          0.687
LGA    H      83      A      28          1.555
LGA    -       -      E      29           -
LGA    -       -      Q      30           -
LGA    H      84      Q      31          0.669
LGA    H      85      K      32          0.391
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -
LGA    -       -      F      41           -
LGA    -       -      R      42           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   42    5.0      5    1.02     0.00     11.717     0.448

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.635708 * X  +  -0.361798 * Y  +  -0.681893 * Z  + -17.438471
  Y_new =   0.640417 * X  +  -0.246001 * Y  +   0.727564 * Z  + -36.223419
  Z_new =  -0.430978 * X  +  -0.899214 * Y  +   0.075317 * Z  +  42.278660 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.487233    1.654360  [ DEG:   -85.2121     94.7879 ]
  Theta =   0.445576    2.696017  [ DEG:    25.5296    154.4704 ]
  Phi   =   0.789088   -2.352504  [ DEG:    45.2114   -134.7886 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0335TS102_2                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS102_2.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   42   5.0    5   1.02    0.00  11.717
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS102_2
PFRMAT TS
TARGET T0335
MODEL 2
PARENT 2aml_A
ATOM      1  N   HIS    81      -0.700   0.806   8.978  1.00  1.00
ATOM      2  CA  HIS    81       0.194   2.009   8.902  1.00  1.00
ATOM      3  C   HIS    81       0.563   2.185   7.422  1.00  1.00
ATOM      4  O   HIS    81       1.139   1.282   6.804  1.00  1.00
ATOM      5  CB  HIS    81       1.496   1.831   9.725  1.00  1.00
ATOM      6  N   HIS    82       0.205   3.331   6.836  1.00  1.00
ATOM      7  CA  HIS    82       0.544   3.649   5.450  1.00  1.00
ATOM      8  C   HIS    82       2.033   3.946   5.387  1.00  1.00
ATOM      9  O   HIS    82       2.533   4.902   6.032  1.00  1.00
ATOM     10  CB  HIS    82      -0.274   4.862   4.994  1.00  1.00
ATOM     11  N   HIS    83       2.745   3.086   4.662  1.00  1.00
ATOM     12  CA  HIS    83       4.147   3.340   4.340  1.00  1.00
ATOM     13  C   HIS    83       4.242   3.345   2.826  1.00  1.00
ATOM     14  O   HIS    83       4.063   2.303   2.194  1.00  1.00
ATOM     15  CB  HIS    83       5.083   2.282   4.945  1.00  1.00
ATOM     16  N   HIS    84       4.426   4.551   2.256  1.00  1.00
ATOM     17  CA  HIS    84       4.389   4.782   0.786  1.00  1.00
ATOM     18  C   HIS    84       5.235   3.768  -0.021  1.00  1.00
ATOM     19  O   HIS    84       4.793   3.303  -1.065  1.00  1.00
ATOM     20  CB  HIS    84       4.855   6.237   0.524  1.00  1.00
ATOM     21  N   HIS    85       6.422   3.429   0.479  1.00  1.00
ATOM     22  CA  HIS    85       7.310   2.547  -0.271  1.00  1.00
ATOM     23  C   HIS    85       7.013   1.068  -0.016  1.00  1.00
ATOM     24  O   HIS    85       7.590   0.221  -0.687  1.00  1.00
ATOM     25  CB  HIS    85       8.777   2.890  -0.010  1.00  1.00
TER
END
