Program : SITE2RT
Version : 971127
Author : Gerard J. Kleywegt & T. Alwyn Jones,
Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : try to find inter-crystal operators from two sets of sites
Package : RAVE
Reference(s) for this program:
* 1 * T.A. Jones (1992). A, yaap, asap, @#*? A set of averaging programs. In "Molecular Replacement", edited by E.J. Dodson, S. Gover and W. Wolf. SERC Daresbury Laboratory, Warrington, pp. 91-105.
* 2 * G.J. Kleywegt & T.A. Jones (1994). Halloween ... Masks and Bones. In "From First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC Daresbury Laboratory, Warrington, pp. 59-66.
* 3 * G.J. Kleywegt & R.J. Read (1997). Not your average density. Structure 5, 1557-1569. [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9438862&form=6&db=m&Dopt=r]
* 4 * G.J. Kleywegt & T.A. Jones (2037 ?). Convenient single and multiple crystal real-space averaging. To be published ???
* 5 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
971125 - 0.1 - first version
971126 - 0.2 - improved
971127 - 0.3 - first released version; manual
SITE2RT tries to find RT-operators (RT = rotation/translation), as needed for multiple crystal form averaging, by inspecting two sets of sites. These sites could be heavy atom positions, or selenium positions, etc.
The input consists of two small PDB files (containing the sites for each crystal form) and a few program parameters:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Max nr of atoms : ( 1000)First PDB file (smallest nr of atoms) ? (m1.pdb) q1.pdb Second PDB file (largest nr of atoms) ? (m2.pdb) q2.pdb
Nr of atoms read file 1 : ( 6)
Nr of atoms read file 2 : ( 13)
Triple distance tolerance ? ( 3.000) 4 Superpositioning tolerance ? ( 3.000) 4 Min nr of matched sites ? ( 4) 4
Exhaustive search (Y/N) ? (Y) n
Output ALL solutions (Y/N) ? (N) y
Start search - may take some time ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The algorithm is very simple:
- enumerate all triples of sites in the first "molecule" (i.e.,
sets of 3 sites)
- for each triple, find all triples in the other "molecule" that
have similar mutual distances (i.e., none of their distances
differ by more than the "triple distance tolerance" from those
in the first triple)
- for each pair of triples, calculate the least-squares operator
and apply it to all the sites of the second "molecule"
- check if there are more sites in the second "molecule" which
are close in space (after applying the operator), within the
"superpositioning tolerance"
- if any additional sites are found, re-calculate the operator
and repeat the check for more matched sites
- at the end, report the best match (highest number of matched
sites and lowest superpositioning RMSD)
If you do NOT do an exhaustive search, sites in "molecule 2" which have been matched will not be used in subsequent matching attempts with other triples. Normally, however, you would do an exhaustive search (unless you have hundreds of sites).
If you want, you can get verbose output for all solutions. You could use this if you want to try more solutions than merely the top-scoring one.
Once the calculations have finished, you can re-run them with different parameters.
In the following example, one crystal form contains 6 sites, and the other 13.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT ***Version - 971127/0.3 (C) 1992-97 Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) 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 - Thu Nov 27 16:45:37 1997 User - gerard Mode - interactive Host - sarek ProcID - 5629 Tty - /dev/ttyq14
*** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT ***
Reference(s) for this program:
* 1 * G.J. Kleywegt, Uppsala University, Uppsala, Sweden, Unpublished program.
* 2 * G.J. Kleywegt & T.A. Jones, Chapter 25.2.6. O and associated programs, Int. Tables for Crystallography, Volume F (1999 ?).
==> For manuals and complete references, visit: ==> http://alpha2.bmc.uu.se/usf/
*** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT ***
Max nr of atoms : ( 1000)
First PDB file (smallest nr of atoms) ? (m1.pdb) q1.pdb Second PDB file (largest nr of atoms) ? (m2.pdb) q2.pdb
Nr of atoms read file 1 : ( 6)
Nr of atoms read file 2 : ( 13)
Triple distance tolerance ? ( 3.000) 4 Superpositioning tolerance ? ( 3.000) 4 Min nr of matched sites ? ( 4)
Exhaustive search (Y/N) ? (Y)
Output ALL solutions (Y/N) ? (N)
Start search - may take some time ! Hit nr 1 *** Nr matched sites = 4 *** RMSD (A) = 4.895 Hit nr 2 *** Nr matched sites = 4 *** RMSD (A) = 2.529 Hit nr 3 *** Nr matched sites = 4 *** RMSD (A) = 2.070 Hit nr 4 *** Nr matched sites = 4 *** RMSD (A) = 3.553 Hit nr 5 *** Nr matched sites = 4 *** RMSD (A) = 2.254 Hit nr 6 *** Nr matched sites = 4 *** RMSD (A) = 2.408 Hit nr 7 *** Nr matched sites = 4 *** RMSD (A) = 1.761 Hit nr 8 *** Nr matched sites = 4 *** RMSD (A) = 1.761
-----------------------------
Nr of hits : ( 8)
-----------------------------
Best hit was nr : ( 7) Nr of matching sites : ( 4) With RMSD (A) : ( 1.761)
Mol 1 Mol 2 Distance --------------- --------------- -------- X HET 2 <--> X HET 10 = 1.795 A X HET 4 <--> X HET 5 = 1.689 A X HET 6 <--> X HET 6 = 1.280 A X HET 5 <--> X HET 3 = 2.166 A
RT Mol 2 --> Mol 1 :
.LSQ_RT_SITE2RT_BEST R 12 (3f16.8) 0.06260084 0.57837784 -0.81336349 0.97134298 0.15192220 0.18279076 0.22929008 -0.80149776 -0.55229282 -2.93325138 41.75638199 47.26410294
Nr of RT operators : 1
RT-OP 1 = 0.0626008 0.9713430 0.2292901 -2.933 0.5783778 0.1519222 -0.8014978 41.756 -0.8133635 0.1827908 -0.5522928 47.264 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 105.965 -123.524 -167.334 Spherical polars Omega Phi Chi 105.326 46.649 131.981 Direction cosines of rotation axis 0.662048 0.701306 -0.264315 Dave Smith -55.430 -144.426 93.687 X-PLOR polars Phi Psi Kappa -158.236 134.532 131.981 Lattmann Theta+ Theta2 Theta- 61.369 123.524 -266.701 Rotation angle 131.981
RT Mol 1 --> Mol 2 :
.LSQ_RT_INVERSE_BEST R 12 (3f16.8) 0.06260084 0.97134298 0.22929008 0.57837784 0.15192220 -0.80149776 -0.81336349 0.18279076 -0.55229282 14.47555351 -12.13396931 60.24383926
Nr of RT operators : 1
RT-OP 1 = 0.0626008 0.5783778 -0.8133635 14.476 0.9713430 0.1519222 0.1827908 -12.134 0.2292901 -0.8014978 -0.5522928 60.244 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 167.334 123.524 -105.965 Spherical polars Omega Phi Chi 74.674 -133.351 131.981 Direction cosines of rotation axis -0.662048 -0.701306 0.264315 Dave Smith -161.687 76.745 -83.823 X-PLOR polars Phi Psi Kappa 21.764 -134.532 131.981 Lattmann Theta+ Theta2 Theta- -61.369 123.524 93.299 Rotation angle 131.981
Re-run with different parameters ? (N)
*** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT ***
Version - 971127/0.3 Started - Thu Nov 27 16:45:37 1997 Stopped - Thu Nov 27 16:46:08 1997
CPU-time taken : User - 0.0 Sys - 0.0 Total - 0.1
*** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT ***
>>>>>> This program: (C) 1992-97, GJ Kleywegt & TA Jones <<<<<< >>>> E-mail: gerard@xray.bmc.uu.se or alwyn@xray.bmc.uu.se <<<< > http://alpha2.bmc.uu.se/usf/gerard_manuals.html <
*** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** SITE2RT *** ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that the best hit is found more than once (stemming from different initial triples).
Note that the best operator is printed "both ways", i.e. as an operator that maps "molecule 2" onto "molecule 1", and as the inverse operator which maps "molecule 1" onto "molecule 2".
None, at present.
Created at Fri Dec 18 19:42:31 1998
by MAN2HTML version 971024/1.6