pales Logo

As described in the paper:

Prediction of sterically induced alignment in a dilute liquid crystalline phase:
aid to protein structure determination by NMR.

Markus Zweckstetter and Ad Bax
J. Am. Chem. Soc. , 122, (2000) 3791-3792
Contact: zweckste@speck.niddk.nih.gov


DOWNLOAD

Sparc Solaris 5.6 version
SGI Irix 6.2 version
RedHat Linux 6.0 version

The download provides a compressed tar archive with a PALES executable and example files. The archive can be unpacked with a command like the following:


   zcat pales.linux.tar.Z | tar xvf -

Users are encouraged to email the author to be informed about updates and related software.



What is PALES?
Components of the PALES Software
Changes to SSIA
How to Use PALES
Data Format
Test Files
A PALES Example Session
About the Name PALES


What is PALES?

PALES is a software for analysis of residual dipolar couplings. Its main component is the PALES (Prediction of ALignmEnt from Structure) simulation that predicts the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein/nucleic acid/oligosaccharide) three-dimensional shape. This can be used to validate the correctness of derived structures, to distinguish monomeric from multimeric structures and to evaluate multiple-conformer models for flexible proteins. In addition, features for analysis of experimental dipolar couplings and dipolar coupling tensors are available, such as best-fitting a dipolar coupling tensor to its corresponding 3D structure.
pales cartoon 2

Components of the PALES Software

The PALES software consists of five modules: These components allow a rapid analysis of weak alignment that can be observed when a macromolecule is dissolved in a dilute liquid crystalline phase (N. Tjandra & A. Bax, Science , 278, (1997) 1111-1114). The components comprise the following:
  1. Prediction of molecular alignment/residual dipolar couplings from first principles (PALES)
    This module comprises the prediction of alignment from structure approach as previously distributed under the name SSIA. PALES predicts the magnitude and orientation of a solute's alignment from its three-dimensional shape. This can be used to validate the correctness of derived structures, to distinguish monomeric from multimeric structures and to evaluate multiple-conformer models for flexible proteins. The only required input is a PDB structure. Using the PDB structure the alignment tensor will be simulated assuming purely steric interaction between the molecule of interest and the liquid crystal particles. From the alignment tensor dipolar couplings can then be predicted. Liquid crystal systems having a dominant steric interaction include bicelles (M. Ottiger & A. Bax, J. Biomol. NMR , 12, (1998) 361-372) and poly(ethylene glycol)-based systems (M. Rueckert & G. Otting, J. Am. Chem. Soc. , 122, (2000) 7793-7797). In cases where electrostatic repulsion plays a major role the orientation of a solute's alignment can also reliably be predicted.

  2. PALES for free format 3D structures
    With this module a PALES simulation based on first principles can be performed for any array of three-dimensional coordinates. No standard PDB format is required. Simulation parameters are accessible in the same way as in 1).

  3. Best-fit of measured dipolar couplings to 3D structure
    The alignment tensor predicted based solely on the three-dimensional structure of a molecule can be compared to one back-calculated from a set of measured residual dipolar couplings. For such a best-fit of observed dipolar couplings to a 3D structure singular value decomposition and non-linear minimization are available. The order matrix analysis of residual dipolar couplings via singular value decomposition is performed as described by J.A. Losonczi, M. Andrec, M.W.F. Fischer and J.H. Prestegard, J. Magn. Reson. , 138, (1999) 334-342. Singular value decomposition only needs a minimum of 5 dipolar couplings, whereas non-linear minimization allows fixing of any of the five parameters describing the alignment tensor during minimization. In addition, this module offers the possibility to predict residual dipolar couplings from a user supplied alignment tensor. The required input is a PDB file and a minimum of five dipolar couplings.

  4. Basic analysis of dipolar coupling tensors
    This module allows manipulation of dipolar coupling tensors. Simple mathematical operations are possible for two dipolar coupling tensors such as addition or multiplication. In addition, back-calculation of Euler angles from an arbitrary symmetric and traceless matrix is possible as well as comparison of two alignment tensors in three and five dimensions. The minimum required input is a matrix with five independent elements.

  5. Basic analysis of dipolar couplings
    This module allows manipulation of two sets of dipolar couplings. Simple mathematical operations are possible for sets of dipolar couplings such as addition or multiplication. In addition, two sets of dipolar couplings can be compared statistically. The required input is at least one table with dipolar couplings.

Changes to SSIA

Besides the new name there are several changes compared to the original SSIA version of the program.
  1. PALES is now fully usable for proteins, nucleic acids and oligosaccharides.
  2. Any type of dipolar coupling can be used.
  3. Parameters for a PALES simulation are controlled by command line arguments.
  4. All standard PDB files can be used including multiple-chain molecules. A broad range of functions (written by Frank Delaglio [Note: as of Spring 2007, Frank is no longer at the NIH; contact Frank at delaglio@nmrscience.com]) for selecting certain parts of a molecule were incorporated. In addition, a separate module is available for performing a PALES simulation on non-standard PDB files.
  5. The input and output format has been unified with the NMRWish/DYNAMO and DC programs by Frank Delaglio.
  6. PALES and the other programs now use the same internuclear distances for the N-HN, CA-HA, CA-C and N-C vectors (M. Ottiger & A. Bax, J. Am. Chem. Soc. , 120, (1998) 12334-12341).
  7. All observed dipolar couplings are now supplied as isotropic - aligned splitting. The negative gyromagnetic ratio of 15N is taken into account within PALES.
  8. Additional features for analysis of experimental dipolar couplings and dipolar coupling tensors were included.

How to Use PALES

Various options are available for the different PALES modules. To start off type
pales -help
This gives you the list of available command line arguments.


The basic use of the currently five available modules is as follows:
  1. Prediction of molecular alignment/residual dipolar couplings from first principles (PALES) [default]

    -stPales
    

  2. PALES for free format 3D structures
    -stPalesFree
    

  3. Best-fit of measured dipolar couplings to 3D structure
    -bestFit
    
    • Singular value decomposition
      pales -bestFit -inD dc_1IGD.tab -pdb 1IGD_H_s.pdb \
            -outD svd.tbl -s1 2 -a1 7 -pdbRot rot.pdb   \
            -map 500 -outMap worldmap.txt
      
      (The '-map' flag is used for mapping the deviation of alignment tensor orientations. These are written to 'worldmap.txt'. 500 iterations are done.)

    • Back-calculation of dipolar couplings from a user supplied order matrix
      pales -bestFit -inD dc_1IGD.tab -pdb 1IGD_H_s.pdb \
            -outD saupePred.tbl -s1 2 -a1 7 \
            -saupe -9.2042e-05  2.3990e-04  3.8255e-04 -4.4549e-04  3.9788e-04
      
      (The order of matrix elements is Szz, Sxx-yy, Sxy, Sxz and Syz.)

    • Back-calculation of residual dipolar couplings for Fixed Da, Dr, and Rotations.
      pales -bestFit -inD dc_1IGD.tab -pdb 1IGD_H_s.pdb \
            -outD dadrFixed.tbl -s1 2 -a1 7 \
            -fixed -da -4.135779e-04 -dr -6.901196e-05  \
            -psi -43.23 -theta 149.43 -phi 81.40
      
    • Non-linear minimization for best alignment orientation with fixed Da & Dr
      pales -bestFit -inD dc_1IGD.tab -pdb 1IGD_H_s.pdb \
            -outD dadrOnlyFixed.tbl -s1 2 -a1 7 \
            -dadr -da -4.135779e-04 -dr -6.901196e-05
      

  4. Basic analysis of dipolar coupling tensors
    -anA
    
    pales -anA -outA anA.tbl \
          -inS1 -8.9631e-05  2.4300e-04  3.8479e-04 -4.4164e-04  3.9631e-04 \
          -inS2 -1.3042e-05  4.1560e-04  3.5832e-04 -4.6099e-04  4.0923e-04
    

  5. Basic analysis of dipolar couplings
    -anDC
    
    pales -anDC -outD anDC.tbl -inD1 dc_1IGD.tab -inD2 dc_1IGD.tab \
          -s1 20 -sN 40
    

Data Format

  1. Input


  2. Output

    If no output files are specified results are written to standard output.

    Following parameters/values are reported:



    To assess a prediction look at the following parameters:


Test Files

1IGD_H_s.pdb PDB file of the protein G domain (shortened by 5 residues and protons added with MOLMOL )
dc_1igd.txt File with measured D(N-HN) dipolar couplings
chkPALES2.1.com Shell script for testing the different modules

In addition, output files from test runs are included. For visualization of alignment tensor distributions the file 'mapTemplate.tab' with the mapping coordinates of the map itself is included ( J.A. Losonczi, M. Andrec, M.W.F. Fischer and J.H. Prestegard, J. Magn. Reson. , 138, (1999) 334-342). The maps can be viewed with the free program Xmgr.


A PALES Example Session

  1. Program call
    pales -pdb 1IGD_H_sDC.pdb -outD ssia.tbl
    

  2. Output (ssia.tbl)
    REMARK Molecular Alignment Simulation.
    
    REMARK Simulation parameters.
    
    DATA PALES_MODE STERIC
    
    DATA PALES LC_TYPE               	wall
    DATA PALES LC_CONCENTRATION 	0.050
    DATA PALES ORIENT_SPHERE       	100
    DATA PALES ORIENT_PSI          	18
    DATA PALES GRID_SPACING        	0.200
    DATA PALES MODEL_RADIUS        	20.000
    DATA PALES LC_ORDER            	0.800
    DATA PALES ATOM_RADIUS         	0.000
    DATA PALES SEL_SIMPLE_FLAG     	0
    DATA PALES SURF_FLAG           	1
    
    REMARK Order matrix.
    
    DATA SAUPE  -8.9631e-05  2.4300e-04  3.8479e-04 -4.4164e-04  3.9631e-04
    
    DATA IRREDUCIBLE REPRESENTATION (A0,A1R,A1I,A2R,A2I)   -3.0583e+00  1.2304e+01  1.1041e+01  3.3849e+00 -1.0720e+01
    DATA IRREDUCIBLE GENERAL_MAGNITUDE   2.8438e+01
    
    REMARK Eigensystem & Euler angles for clockwise rotation about z, y', z''.
    
    DATA EIGENVALUES (Axx,Ayy,Azz)    3.0889e-04  5.1593e-04 -8.2482e-04
    DATA EIGENVECTORS
    DATA EIGENVECTORS XAXIS  1.2036e-01  7.6741e-01  6.2976e-01
    DATA EIGENVECTORS YAXIS  8.5264e-01  2.4500e-01 -4.6150e-01
    DATA EIGENVECTORS ZAXIS -5.0845e-01  5.9250e-01 -6.2483e-01
    
    DATA Q_EULER_SOLUTIONS    ALPHA     BETA    GAMMA
    DATA Q_EULER_ANGLES  1   323.77   128.67    49.37
    DATA Q_EULER_ANGLES  2   143.77   128.67    49.37
    DATA Q_EULER_ANGLES  3   216.23    51.33   229.37
    DATA Q_EULER_ANGLES  4    36.23    51.33   229.37
    
    
    REMARK Euler angles (psi/theta/phi) for rotation about x, y, z.
    
    DATA EULER_SOLUTIONS 2
    DATA EULER_ANGLES  -43.48  149.44   81.97
    DATA EULER_ANGLES  136.52   30.56  261.97
    
    DATA Da -4.124083e-04
    DATA Dr -6.901216e-05
    
    
    REMARK Dipolar couplings.
    
    DATA N                    		41
    DATA RMS                  		1.222
    DATA Chi2                 		61.223
    DATA CORR R               	0.996
    DATA CORNILESCU Q         	0.120
    DATA REGRESSION OFFSET    	-0.739 +/- 0.148 [Hz]
    DATA REGRESSION SLOPE     		0.977 +/- 0.015 [Hz]
    DATA REGRESSION BAX SLOPE 	0.981 +/- 0.010 [Hz]
    
    VARS    RESID_I RESNAME_I ATOMNAME_I RESID_J RESNAME_J ATOMNAME_J DI D_OBS D D_DIFF DD W
    FORMAT  %4d %4s %4s %4d %4s %4s %9.2f %9.3f %9.3f %9.3f %.2f %.2f
    
        2  THR   HN    2  THR    N -21523.10    1.4640    0.0857    1.3783  1.0000 1.00
        3  TYR   HN    3  TYR    N -21523.10    7.0570    7.8340   -0.7770  1.0000 1.00
        4  LYS   HN    4  LYS    N -21523.10    8.6540    7.3118    1.3422  1.0000 1.00
        5  LEU   HN    5  LEU    N -21523.10   12.1800   10.9437    1.2363  1.0000 1.00
        7  LEU   HN    7  LEU    N -21523.10   12.6910   10.0725    2.6185  1.0000 1.00
        8  ASN   HN    8  ASN    N -21523.10    5.2020    4.5600    0.6420  1.0000 1.00
       12  LEU   HN   12  LEU    N -21523.10   11.6770   10.3776    1.2994  1.0000 1.00
       14  GLY   HN   14  GLY    N -21523.10   10.5530   11.0063   -0.4533  1.0000 1.00
       15  GLU   HN   15  GLU    N -21523.10   11.1540    9.9303    1.2237  1.0000 1.00
       16  THR   HN   16  THR    N -21523.10   11.0090   10.3052    0.7038  1.0000 1.00
       17  THR   HN   17  THR    N -21523.10    8.8740    8.1451    0.7289  1.0000 1.00
       18  THR   HN   18  THR    N -21523.10    5.5190    5.7485   -0.2295  1.0000 1.00
       19  GLU   HN   19  GLU    N -21523.10    5.6510    6.1800   -0.5290  1.0000 1.00
       20  ALA   HN   20  ALA    N -21523.10    4.1730    4.9946   -0.8216  1.0000 1.00
       21  VAL   HN   21  VAL    N -21523.10    4.7990    4.5163    0.2827  1.0000 1.00
       22  ASP   HN   22  ASP    N -21523.10   -4.2940   -4.4661    0.1721  1.0000 1.00
       23  ALA   HN   23  ALA    N -21523.10   -2.3260   -2.5724    0.2464  1.0000 1.00
       24  ALA   HN   24  ALA    N -21523.10  -13.4330  -15.2750    1.8420  1.0000 1.00
       25  THR   HN   25  THR    N -21523.10  -10.5960  -12.4346    1.8386  1.0000 1.00
       26  ALA   HN   26  ALA    N -21523.10   -5.4130   -6.6161    1.2031  1.0000 1.00
       28  LYS   HN   28  LYS    N -21523.10  -16.1580  -16.7218    0.5638  1.0000 1.00
       30  PHE   HN   30  PHE    N -21523.10   -8.6620   -8.3276   -0.3344  1.0000 1.00
       31  LYS   HN   31  LYS    N -21523.10  -13.9680  -14.9181    0.9501  1.0000 1.00
       32  GLN   HN   32  GLN    N -21523.10  -16.0390  -16.6349    0.5959  1.0000 1.00
       33  TYR   HN   33  TYR    N -21523.10  -12.0490  -12.6305    0.5815  1.0000 1.00
       34  ALA   HN   34  ALA    N -21523.10   -9.6080  -10.3609    0.7529  1.0000 1.00
       35  ASN   HN   35  ASN    N -21523.10  -15.6960  -16.4080    0.7120  1.0000 1.00
       36  ASP   HN   36  ASP    N -21523.10  -15.0910  -14.7718   -0.3192  1.0000 1.00
       37  ASN   HN   37  ASN    N -21523.10   -3.6870   -3.9808    0.2938  1.0000 1.00
       38  GLY   HN   38  GLY    N -21523.10   -8.0650   -6.7237   -1.3413  1.0000 1.00
       44  THR   HN   44  THR    N -21523.10   11.6760    9.1670    2.5090  1.0000 1.00
       45  TYR   HN   45  TYR    N -21523.10   11.8120   10.9110    0.9010  1.0000 1.00
       46  ASP   HN   46  ASP    N -21523.10   10.7600    9.6707    1.0893  1.0000 1.00
       47  ASP   HN   47  ASP    N -21523.10   11.0430   10.4336    0.6094  1.0000 1.00
       49  THR   HN   49  THR    N -21523.10    2.4570    0.0918    2.3652  1.0000 1.00
       50  LYS   HN   50  LYS    N -21523.10    8.5140    7.4738    1.0402  1.0000 1.00
       51  THR   HN   51  THR    N -21523.10    9.3680    9.1265    0.2415  1.0000 1.00
       52  PHE   HN   52  PHE    N -21523.10   11.5930   10.7652    0.8278  1.0000 1.00
       53  THR   HN   53  THR    N -21523.10   10.1490    8.8621    1.2869  1.0000 1.00
       54  VAL   HN   54  VAL    N -21523.10   12.2240    9.9134    2.3106  1.0000 1.00
       56  GLU   HN   56  GLU    N -21523.10   11.6220    9.1445    2.4775  1.0000 1.00
    

About the Name PALES

Pales is the Roman patron goddess of shepherds and flocks. Pales also presides over the health and fertility of the domestic animals. Her festival is the Palilia (also called the Parilia) and was celebrated by shepherds on April 21, the legendary founding date of Rome. On that day large fires were made through which they drove the cattle.

roman coin

Subsequently, an asteroid (discovered September 19th 1857) and a butterfly ( Boloria pales ) was named after the goddess.