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.
pales -helpThis gives you the list of available command line arguments.
-stPales
pales -pdb 1IGD_H_sDC.pdb(Default simulation parameters are used and results are written to standard output; the magnitude of alignment scales linearly with concentration and for molecules with dimensions of roughly the rod radius alignment tensors for the wall and the rod model are collinear.)
pales -inD dc_1IGD.tab -pdb 1IGD_H_s.pdb -outD ssiaB.tbl \ -s1 2 -a1 7 -pdbRot rot.pdb( '-s1' and '-a1' are used for specifying an offset of 5 between the PDB file and the sequence number of the measured residual dipolar couplings; with '-pdbRot' a PDB file is written out that is rotated in such a way that the axes of the alignment tensor are parallel to the laboratory frame.)
pales -inD dc_1IGD.tab -pdb 1IGD_H_s.pdb -outD ssiaC.tbl \ -s1 2 -a1 7 -r1 10 -rN 60 \ -bic -wv 0.03 -dGrid 0.3 -dot 133 -digPsi 23 -rM 33.0 \ -lcS 0.83 -rA 0.3 -H -nosurf('-r1' and '-rN' are used for selection of residues 10 to 60 in the simulation.)
-stPalesFree
pales -stPalesFree -pdbF 1IGD_H_s.pdb -outA ssiaF.tbl
pales -stPalesFree -pdbF 1IGD_H_s.pdb -outA ssiaF.tbl \ -bic -wv 0.03 -dGrid 0.3 -dot 133 -digPsi 23 -rM 33.0 \ -lcS 0.83 -rA 0.3 -H -nosurf
-bestFit
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.)
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.)
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
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
-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
-anDC
pales -anDC -outD anDC.tbl -inD1 dc_1IGD.tab -inD2 dc_1IGD.tab \ -s1 20 -sN 40
DATA SEQUENCE MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL DATA SEQUENCE EDGRTLSDYN IQKESTLHLV LRLRGG VARS RESID_I RESNAME_I ATOMNAME_I RESID_J RESNAME_J ATOMNAME_J D DD W FORMAT %5d %6s %6s %5d %6s %6s %9.3f %9.3f %.2f 2 GLN N 2 GLN HN -15.524 1.000 1.00 3 ILE N 3 ILE HN 10.521 1.000 1.00 4 PHE N 4 PHE HN 9.648 1.000 1.00 5 VAL N 5 VAL HN 6.082 1.000 1.00 1 MET C 2 GLN HN 3.993 0.333 3.00 2 GLN C 3 ILE HN -5.646 0.333 3.00 3 ILE C 4 PHE HN 1.041 0.333 3.00 4 PHE C 5 VAL HN 0.835 0.333 3.00 1 MET C 2 GLN N 2.651 0.125 8.00 2 GLN C 3 ILE N -3.768 0.125 8.00 3 ILE C 4 PHE N 1.463 0.125 8.00 4 PHE C 5 VAL N -1.726 0.125 8.00 2 GLN N 2 GLN HN -15.524 1.000 1.00 3 ILE N 3 ILE HN 10.521 1.000 1.00 4 PHE N 4 PHE HN 9.648 1.000 1.00 5 VAL N 5 VAL HN 6.082 1.000 1.00 1 MET HA 1 MET CA -38.341 1.000 0.50 2 GLN HA 2 GLN CA 11.662 1.000 0.50 3 ILE HA 3 ILE CA 18.424 1.000 0.50 4 PHE HA 4 PHE CA 26.733 1.000 0.50
alpha | Clockwise rotation around z, leading to new system x',y',z' |
beta | Clockwise rotation around y', leading to new system x'',y'',z'' |
gamma | Clockwise rotation around z'' |
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 |
pales -pdb 1IGD_H_sDC.pdb -outD 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