Program : FINDNCS
Version : 060503
Author : Gerard J. Kleywegt & T. Alwyn Jones,
Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 596,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : find NCS operators in sets of atoms
Package : RAVE
Reference(s) for this program:
* 1 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.
960821 - 0.1 - first version
960822 - 0.2 - second version
960823 - 0.3 - third version
2006-05-03 - 0.4 - first released version
FINDNCS takes as input a PDB file and tries to find NCS operators relating subsets of the atoms in the file. It was written back in 1996 and not released until ten years later. I have never tested it on real cases, so I make no claims as to its utility. There are newer and much cleverer programs around.
The input file was generated by taking the CA atoms of all LEU residues in PDB entry 1LDN (8-fold NCS), sorted by Z-coordinate.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 983 gerard sarek 17:28:09 average/test > ../6d/6D_FINDNCS*** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS ***
Version - 060503/0.4 (c) 1992-2005 Gerard J. Kleywegt, Dept. Cell Mol. Biol., Uppsala (SE) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Wed May 3 17:50:19 2006 User - gerard Mode - interactive Host - sarek (Irix/SGI) ProcID - 16860 Tty - /dev/ttyq5
*** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS ***
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-2005). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.
==> For manuals and up-to-date references, visit: ==> http://xray.bmc.uu.se/usf ==> For reprints, visit: ==> http://xray.bmc.uu.se/gerard ==> For downloading up-to-date versions, visit: ==> ftp://xray.bmc.uu.se/pub/gerard
*** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS ***
Maximum number of atoms : ( 2000)
Input PDB file ? (user.pdb) findncs_test.pdb Input PDB file : (findncs_test.pdb)
Nr of atoms read : ( 184)
Min nr of atoms to match ? ( 3) 5 Nr of RT-operators total ? ( 2) 7 Max initial triple RMSD ? ( 2.000) Min initial triple RMSD ? ( 0.001) Atom-matching tolerance ? ( 2.000) Min dist RT-related atoms ? ( 1.000) Min dist intra-mol atoms ? ( 2.000) Max dist intra-mol atoms ? ( 100.000) 30
Min nr of atoms to match : ( 5) Nr of RT-operators total : ( 7) Max initial triple RMSD : ( 2.000) Min initial triple RMSD : ( 0.001) Atom-matching tolerance : ( 2.000) Min dist RT-related atoms : ( 1.000) Min dist intra-mol atoms : ( 2.000) Max dist intra-mol atoms : ( 30.000)
Triple : ( 1) | CA LEU A 153 | CA LEU A 279 | CA LEU A 276 | 20.24 15.44 5.77 Nr of nearby atoms : ( 13)
Triple : ( 1) Trials : ( 3540) Best match for triple : ( 1) RMSD (A) : ( 0.196) Operator : ( -0.829 0.187 -0.527 0.271 -0.690 -0.672 - 0.489 -0.700 0.521 61.787 2.642 21.695) Match | CA LEU A 153 | ... | CA LEU B 153 | Match | CA LEU A 279 | ... | CA LEU B 279 | Match | CA LEU A 276 | ... | CA LEU B 276 | Match | CA LEU A 325 | ... | CA LEU B 325 | Distance 0.91 A RMSD now : ( 0.196) Match | CA LEU A 321 | ... | CA LEU B 321 | Distance 0.38 A RMSD now : ( 0.229) Match | CA LEU C 214 | ... | CA LEU D 214 | Distance 1.02 A RMSD now : ( 0.330) Match | CA LEU A 143 | ... | CA LEU B 143 | Distance 0.28 A RMSD now : ( 0.319)
[...]
Match | CA LEU C 153 | ... | CA LEU D 153 | Distance 0.31 A RMSD now : ( 0.310) Nr of matched atoms : ( 46) Found one !
Nr of RT operators : 1
RT-OP 1 = -0.8190150 0.2284013 -0.5263526 60.955 0.2236608 -0.7177015 -0.6594545 2.773 -0.5283844 -0.6578276 0.5367239 22.152 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 51.404 -57.539 128.772 Spherical polars Omega Phi Chi 151.230 51.316 179.844 Direction cosines of rotation axis 0.300820 0.375698 -0.876563 X-PLOR polars Phi Psi Kappa -108.941 112.067 179.844 Lattmann Theta+ Theta2 Theta- -180.177 57.539 102.632 Rotation angle 179.844 Nr of atoms left : ( 138)
Triple : ( 1) Trials : ( 10294) Best match for triple : ( 1) RMSD (A) : ( 0.138) Operator : ( 0.202 0.974 -0.104 -0.977 0.193 -0.092 - 0.070 0.121 0.990 59.026 41.793 41.987) Match | CA LEU A 153 | ... | CA LEU G 153 | Match | CA LEU A 279 | ... | CA LEU G 279 | Match | CA LEU A 276 | ... | CA LEU G 276 | Nr of matched atoms : ( 3)
Triple : ( 2) | CA LEU A 153 | CA LEU A 279 | CA LEU A 325 | 20.24 18.51 18.87 Nr of nearby atoms : ( 12)
Triple : ( 2) Trials : ( 10803) Best match for triple : ( 2) RMSD (A) : ( 0.195) Operator : ( 0.192 0.977 -0.088 -0.978 0.183 -0.099 - 0.080 0.105 0.991 59.036 41.491 41.748) Match | CA LEU A 153 | ... | CA LEU G 153 | Match | CA LEU A 279 | ... | CA LEU G 279 | Match | CA LEU A 325 | ... | CA LEU G 325 | Match | CA LEU A 276 | ... | CA LEU G 276 | Distance 0.11 A RMSD now : ( 0.175) Match | CA LEU A 321 | ... | CA LEU G 321 | Distance 0.18 A RMSD now : ( 0.167) Match | CA LEU C 214 | ... | CA LEU E 214 | Distance 0.82 A RMSD now : ( 0.263)
[...]
Match | CA LEU C 153 | ... | CA LEU E 153 | Distance 0.12 A RMSD now : ( 0.328) Nr of matched atoms : ( 46) Found one !
Nr of RT operators : 1
RT-OP 1 = 0.2104992 -0.9732844 -0.0916917 58.589 0.9750976 0.2023375 0.0907966 41.217 -0.0698183 -0.1085210 0.9916392 41.589 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 135.281 7.414 -57.244 Spherical polars Omega Phi Chi 5.876 -173.737 78.332 Direction cosines of rotation axis -0.101762 -0.011167 0.994746 X-PLOR polars Phi Psi Kappa 84.159 -90.640 78.332 Lattmann Theta+ Theta2 Theta- -78.037 7.414 12.525 Rotation angle 78.332 Nr of atoms left : ( 92)
Triple : ( 2) Trials : ( 12606) Best match for triple : ( 2) RMSD (A) : ( 0.332) Operator : ( -0.519 0.700 0.490 0.720 0.050 0.692 0.460 0.712 -0.530 37.991 -30.455 8.246) Match | CA LEU A 153 | ... | CA LEU C 153 | Match | CA LEU A 279 | ... | CA LEU C 279 | Match | CA LEU A 325 | ... | CA LEU C 325 | Nr of matched atoms : ( 3)
Triple : ( 3) | CA LEU A 153 | CA LEU A 279 | CA LEU A 321 | 20.24 21.16 16.11 Nr of nearby atoms : ( 13)
Triple : ( 3) Trials : ( 12296) Best match for triple : ( 3) RMSD (A) : ( 0.214) Operator : ( -0.503 0.715 0.486 0.721 0.038 0.692 0.476 0.698 -0.535 38.085 -31.033 8.191) Match | CA LEU A 153 | ... | CA LEU C 153 | Match | CA LEU A 279 | ... | CA LEU C 279 | Match | CA LEU A 321 | ... | CA LEU C 321 | Match | CA LEU A 276 | ... | CA LEU C 276 | Distance 0.31 A RMSD now : ( 0.228) Match | CA LEU A 325 | ... | CA LEU C 325 | Distance 0.63 A RMSD now : ( 0.302) Match | CA LEU C 214 | ... | CA LEU A 214 | Distance 0.92 A RMSD now : ( 0.371)
[...]
Match | CA LEU A 165 | ... | CA LEU C 165 | Distance 0.24 A RMSD now : ( 0.380) Nr of matched atoms : ( 22) Found one !
Nr of RT operators : 1
RT-OP 1 = -0.5192801 0.7154667 0.4673919 38.032 0.7147201 0.0637367 0.6965002 -30.939 0.4685328 0.6957332 -0.5444558 8.100 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 56.136 122.987 123.958 Spherical polars Omega Phi Chi 61.494 56.089 179.950 Direction cosines of rotation axis 0.490265 0.729293 0.477255 X-PLOR polars Phi Psi Kappa -44.228 -136.827 179.949 Lattmann Theta+ Theta2 Theta- 179.906 122.987 112.178 Rotation angle 179.952 Nr of atoms left : ( 70)
Triple : ( 3) Trials : ( 3218) Best match for triple : ( 3) RMSD (A) : ( 0.367) Operator : ( -0.324 -0.797 -0.510 0.817 0.036 -0.575 0.476 -0.603 0.639 66.473 103.330 59.133) Match | CA LEU A 153 | ... | CA LEU H 153 | Match | CA LEU A 279 | ... | CA LEU H 279 | Match | CA LEU A 321 | ... | CA LEU H 321 | Match | CA LEU A 39 | ... | CA LEU H 39 | Distance 0.41 A RMSD now : ( 0.332) Match | CA LEU D 39 | ... | CA LEU E 39 | Distance 0.29 A RMSD now : ( 0.312) Nr of matched atoms : ( 5) Found one !
Nr of RT operators : 1
RT-OP 1 = -0.3268324 0.8187553 0.4720381 66.446 -0.7981563 0.0283374 -0.6017833 103.313 -0.5060896 -0.5734426 0.6442332 59.213 Determinant of rotation matrix 0.999999 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 128.111 -49.892 131.430 Spherical polars Omega Phi Chi 148.818 88.340 109.095 Direction cosines of rotation axis 0.014995 0.517539 -0.855528 X-PLOR polars Phi Psi Kappa -91.004 121.167 109.095 Lattmann Theta+ Theta2 Theta- 100.460 49.892 -183.319 Rotation angle 109.095 Nr of atoms left : ( 65)
Triple : ( 3) Trials : ( 14446) Best match for triple : ( 3) RMSD (A) : ( 0.248) Operator : ( 0.978 0.130 0.166 0.126 -0.991 0.032 0.169 -0.010 -0.986 32.947 68.288 63.538) Match | CA LEU A 153 | ... | CA LEU F 153 | Match | CA LEU A 279 | ... | CA LEU F 279 | Match | CA LEU A 321 | ... | CA LEU F 321 | Nr of matched atoms : ( 3)
Triple : ( 4) | CA LEU A 153 | CA LEU A 279 | CA LEU A 143 | 20.24 14.48 20.58 Nr of nearby atoms : ( 13)
Triple : ( 4) Trials : ( 14432) Best match for triple : ( 4) RMSD (A) : ( 0.092) Operator : ( 0.981 0.135 0.137 0.130 -0.990 0.047 0.142 -0.029 -0.989 32.276 67.784 63.856) Match | CA LEU A 153 | ... | CA LEU F 153 | Match | CA LEU A 279 | ... | CA LEU F 279 | Match | CA LEU A 143 | ... | CA LEU F 143 | Match | CA LEU A 276 | ... | CA LEU F 276 | Distance 0.28 A RMSD now : ( 0.137) Match | CA LEU A 325 | ... | CA LEU F 325 | Distance 0.23 A RMSD now : ( 0.148) Match | CA LEU A 321 | ... | CA LEU F 321 | Distance 0.65 A RMSD now : ( 0.263)
[...]
Match | CA LEU A 165 | ... | CA LEU F 165 | Distance 0.33 A RMSD now : ( 0.341) Nr of matched atoms : ( 22) Found one !
Nr of RT operators : 1
RT-OP 1 = 0.9799042 0.1341605 0.1476103 32.538 0.1419561 -0.9889141 -0.0435624 67.673 0.1401295 0.0636411 -0.9880859 63.711 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 163.558 -171.147 -24.426 Spherical polars Omega Phi Chi 85.851 3.992 176.912 Direction cosines of rotation axis 0.994995 0.069432 0.072354 X-PLOR polars Phi Psi Kappa 175.841 93.981 176.912 Lattmann Theta+ Theta2 Theta- 220.868 171.147 7.983 Rotation angle 176.912 Nr of atoms left : ( 43)
Triple : ( 4) Trials : ( 5724) Sorry - no triples found
Triple : ( 5) | CA LEU A 153 | CA LEU A 279 | CA LEU A 132 | 20.24 8.87 22.38 Nr of nearby atoms : ( 13)
Triple : ( 5) Trials : ( 5592) Sorry - no triples found
[...]
Triple : ( 24) Trials : ( 5460) Sorry - no triples found
Triple : ( 25) | CA LEU A 153 | CA LEU A 276 | CA LEU A 263 | 15.44 18.71 23.94 Nr of nearby atoms : ( 11)
Triple : ( 25) Trials : ( 5275) Best match for triple : ( 25) RMSD (A) : ( 1.677) Operator : ( -0.708 -0.391 0.588 0.507 0.299 0.809 - 0.492 0.870 -0.014 64.604 114.250 40.122) Match | CA LEU A 153 | ... | CA LEU H 165 | Match | CA LEU A 276 | ... | CA LEU H 134 | Match | CA LEU A 263 | ... | CA LEU H 306 | Match | CA LEU A 279 | ... | CA LEU H 132 | Distance 1.44 A RMSD now : ( 1.570) Match | CA LEU A 91 | ... | CA LEU H 198 | Distance 1.35 A RMSD now : ( 1.484) Match | CA LEU A 270 | ... | CA LEU H 276 | Distance 0.74 A RMSD now : ( 1.375) Nr of matched atoms : ( 6) Found one !
Nr of RT operators : 1
RT-OP 1 = -0.7231784 0.5107784 -0.4648854 65.600 -0.3789006 0.2693591 0.8853700 114.330 0.5774490 0.8164257 -0.0012605 40.289 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 117.703 90.072 125.271 Spherical polars Omega Phi Chi 130.420 -93.784 136.681 Direction cosines of rotation axis -0.050246 -0.759647 -0.648392 X-PLOR polars Phi Psi Kappa -85.569 -139.433 136.681 Lattmann Theta+ Theta2 Theta- 117.026 90.072 172.431 Rotation angle 136.681 Nr of atoms left : ( 37)
Nr of operators found : ( 6)
*** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS ***
Version - 060503/0.4 Started - Wed May 3 17:50:19 2006 Stopped - Wed May 3 17:51:18 2006
CPU-time taken : User - 25.5 Sys - 1.6 Total - 27.1
*** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS ***
>>>>>>>>>>>>>> USF .... Uppsala Software Factory <<<<<<<<<<<<<< >>>>>>>>>> This program: (c) 1992-2005, G J Kleywegt <<<<<<<<<< >>>>>>>>>>>>>>>> E-mail: gerard@xray.bmc.uu.se <<<<<<<<<<<<<<<< >>>>>>>>>>>>>>>>>> http://xray.bmc.uu.se/usf <<<<<<<<<<<<<<<<<<
*** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** FINDNCS *** ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Thu May 4 17:57:44 2006
by MAN2HTML version 060130/2.0.7 . This manual
describes FINDNCS, a program of the Uppsala
Software Factory (USF), written and maintained by Gerard Kleywegt. © 1992-2006.