Program : PACMAN
Version : 961121
Author : Gerard J. Kleywegt, 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 : analyse packing due to (non-)crystallographic symmetry
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (1996). Making the most of your search model. CCP4/ESF-EACBM Newsletter on Protein Crystallography 32, June 1996, pp. 32-36. [http://alpha2.bmc.uu.se/usf/factory_6.html]
* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
940327 - 0.1 - initial version
940328 - 0.2 - a bit more
940707 - 0.3 - changed for use with Eleanor's latest AMORE version
950121 - 0.4 - added two-molecule scan option
951022 - 0.5 - made sensitive to OSYM environment variable
961121 - 0.6 - minor bug fix
PACMAN is a little utility program to help you separate the men from the boys during tedious molecular replacement exercises. It can be used to:
- 1 - test if a molecular replacement solution leads to
clashes between molecule related by (non-)crystallographic
symmetry
- 2 - check out which fraction of the unit cell can in
principle be a solution from a packing point of view
(one- or two-molecule only)
- 3 - compare rotational relations between various solutions
of the AMORE rotation function (a hack of Eleanor
Dodson's ROTPRD program)
- 4 - filter AMORE translation function solutions so that
only those which have reasonable packing survive
The algorithm to test for clashes is extremely simple (which
makes it fast):
- your molecule is approximated as a SPHERE
- expansion under NCS and SGS is carried out
- distances between the centres-of-gravity are tested
If your search model is not approximately spherical, you'll
have to use a more liberal distance cut-off.
NOTE: this program is sensitive to the environment variable OSYM.
It should point to your local copy of $ODAT/symm, the directory
which contains the spacegroup symmetry operators in O format.
When asked for a file with spacegroup operators in O format,
you may either provide a filename, or the name of a sapcegroup
(including blanks if you like, case doesn't matter). The program
will try to open the following files, assuming that STRING is the
what you input:
(1) open a file called STRING
(2) if this fails, check if OSYM is defined and open $OSYM/STRING
(3) if this fails, open $OSYM/string.sym
(4) if this fails, open $OSYM/string.o
Hint: if you make soft links in the OSYM directory, you can also type
spacegroup numbers (e.g.: \ln -s p212121.sym 19.sym).
When you start the program, you'll see the following:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- <133 alien.bmc.uu.se amore/combi> run pacman... Run pacman
... Executing /nfs/public/ALPHA/bin/al_pacman ... For gerard on alien at Fri May 13 19:20:59 MET DST 1994
*** PACMAN *** PACMAN *** PACMAN *** PACMAN *** PACMAN *** PACMAN ***
Version - 940328/0.2 (C) 1993/4 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, etc. etc.
Started - Fri May 13 19:21:00 1994 User - gerard Mode - interactive Host - ALPHA/OSF1 ProcID - 9123 Tty - /dev/ttyp7
*** PACMAN *** PACMAN *** PACMAN *** PACMAN *** PACMAN *** PACMAN ***
Unit cell ? ( 100.000 100.000 100.000 90.000 90.000 90.000) 41.36 41.36 202.71 90.0 90.0 90.0
O spacegroup symmetry operator file ? (symop.o) p43.sym Opening O datablock : (p43.sym) Datablock : (.SPACE_GROUP_OPERATORS) Data type : (R) Number : (48) Format : ((3F10.5))
Nr of spacegroup symmetry operators : 4 SYMOP 1 = 1.0000 0.0000 0.0000 0.000 0.0000 1.0000 0.0000 0.000 0.0000 0.0000 1.0000 0.000 Determinant of rotation matrix = 1.000000 Rotation angle = 0.000000 SYMOP 2 = -1.0000 0.0000 0.0000 0.000 0.0000 -1.0000 0.0000 0.000 0.0000 0.0000 1.0000 0.500 Determinant of rotation matrix = 1.000000 Rotation angle = 180.000000 SYMOP 3 = 0.0000 -1.0000 0.0000 0.000 1.0000 0.0000 0.0000 0.000 0.0000 0.0000 1.0000 0.750 Determinant of rotation matrix = 1.000000 Rotation angle = 90.000000 SYMOP 4 = 0.0000 1.0000 0.0000 0.000 -1.0000 0.0000 0.0000 0.000 0.0000 0.0000 1.0000 0.250 Determinant of rotation matrix = 1.000000 Rotation angle = 90.000000
Centre-of-gravity of search model ? ( 0.000 0.000 0.000)
Nr of molecules per asymmetric unit ? ( 1) 2
Min safe distance should be slightly less than the shortest diameter of your search model. Min safe distance ? ( 25.000) 20
Fractional centre-of-gravity : ( 0.000 0.000 0.000)
Select one of the following options: 0 = quit 1 = try a translation function solution 2 = alter parameters 3 = one-molecule unit-cell scan 4 = ROTPRD (Eleanor Dodson) 5 = test many AMORE TF solutions 6 = two-molecule unit-cell scan (SLOW!)
Option ? ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 1) 1 Molecule : ( 1) Fractional translation ? ( 0.000 0.000 0.000) 0.11177 0.58948 0.00000 Molecule : ( 2) Fractional translation ? ( 0.000 0.000 0.000) 0.76831 0.01983 0.83652 Nr of molecules : ( 216) Expected number : ( 216)Nr of clashes : ( 0) Closest distance : ( 23.260)
Select one of the following options: 0 = quit 1 = try a translation function solution 2 = alter parameters 3 = one-molecule unit-cell scan 4 = ROTPRD (Eleanor Dodson) 5 = test many AMORE TF solutions
Option ? ( 1) Molecule : ( 1) Fractional translation ? ( 0.112 0.589 0.000) 0.11177 0.58948 0.00000 Molecule : ( 2) Fractional translation ? ( 0.768 0.020 0.837) 0.10429 0.47090 0.99584 Nr of molecules : ( 216) Expected number : ( 216)
BANG !!! @ 4.99 A Copy-Mol-Oper-Cell 14 1 1 0 & Copy-Mol-Oper-Cell 40 2 1 -4 Cart 4.62 24.38 0.00 & 4.31 19.48 -0.84 Frac 0.1118 0.5895 0.0000 & 0.1043 0.4709 -0.0042 BANG !!! @ 4.99 A Copy-Mol-Oper-Cell 68 1 2 0 & Copy-Mol-Oper-Cell 95 2 2 0 Cart 36.74 16.98 101.36 & 37.05 21.88 100.51 Frac 0.8882 0.4105 0.5000 & 0.8957 0.5291 0.4958 BANG !!! @ 4.99 A Copy-Mol-Oper-Cell 122 1 3 0 & Copy-Mol-Oper-Cell 149 2 3 0 Cart 16.98 4.62 152.03 & 21.88 4.31 151.19 Frac 0.4105 0.1118 0.7500 & 0.5291 0.1043 0.7458 BANG !!! @ 4.99 A Copy-Mol-Oper-Cell 176 1 4 0 & Copy-Mol-Oper-Cell 203 2 4 0 Cart 24.38 36.74 50.68 & 19.48 37.05 49.83 Frac 0.5895 0.8882 0.2500 & 0.4709 0.8957 0.2458
Nr of clashes : ( 4) Closest distance : ( 4.986) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 1) 3 Step size (A) ? ( 5.000) Nr of steps : ( 9 9 42) Step sizes : ( 1.111E-01 1.111E-01 2.381E-02) #Tried 1000 #Okay 1000 % 100.0 Max dist 41.36 #Tried 2000 #Okay 2000 % 100.0 Max dist 41.36 #Tried 3000 #Okay 3000 % 100.0 Max dist 41.36Positions tried : ( 3402) No clashes for : ( 3402) % of cell okay : ( 100.000) Max distance : ( 41.360) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 3) 4***** ROTPRD ***** By Eleanor Dodson ***** Mod GJK *****
This program reads one basic rotation operator and an unlimited number of secondary operators. Each operator can be input in different ways; each is converted to different conventions. In addition, the basic operator is multiplied by each of the secondary operators in turn, and the resulting operator is also converted to each of the implemented conventions.
Each input line should contain an integer code and up to nine real or integer arguments:
code = 0 => stop the program code = 1 => followed by Crowther ALPHA BETA GAMMA code = 2 => followed by Polar OMEGA PHI CHI code = 3 => followed by three direction cosines L1, L2, L3 and the rotation angle CHI about the axis code = 4 => followed by nine rotation matrix elements in the order R11 R12 R13 R21 ... The product operators are: Rbasic * Rsecondary and: Rbasic * INV(Rsecondary)
Enter code & operator 1 ... 1 34.07 87.82 53.97
PLEASE REMEMBER !! PATTERSON SPHERICAL POLARS OMEGA PHI CHI OMEGA TO AXIS ZO PHI FROM AXIS XO TO AXIS YO NCODE =1 ORTHOG AXES HAVE A ALONG XO CSTAR ALONG ZO NCODE =2 ORTHOG AXES HAVE B ALONG XO ASTAR ALONG ZO NCODE =3 ORTHOG AXES HAVE C ALONG XO BSTAR ALONG ZO ALPHA BETA GAMMA IS IDENTICAL TO ALPHA+PI -BETA GAMMA+PI WHEN BETA = 0 CAN ONLY DEFINE ALPHA + GAMMA WHEN BETA = 180 CAN ONLY DEFINE GAMMA - ALPHA
Matrix nr & determinant .. 1 1.000000 -0.43451 -0.35500 0.82775 0.68243 0.47001 0.55980 -0.58778 0.80812 0.03804
CROWTHER ALPHA BETA GAMMA 34.07003 87.82007 53.97004 SPHERICAL POLARS OMEGA PHI CHI 54.17582 80.05006 117.59576 DIRECTION COSINES OF ROTATION AXIS 0.14010 0.79862 0.58530 DAVE SMITH -86.11273 125.99995 140.75081
Enter code & operator 2 ... 1 27.48 90.12 238.14
Matrix nr & determinant .. 2 1.000000 0.39290 0.24199 0.88717 -0.75300 -0.46911 0.46144 0.52784 -0.84934 -0.00209
CROWTHER ALPHA BETA GAMMA 27.48002 90.12007 -121.86010 SPHERICAL POLARS OMEGA PHI CHI 126.20708 164.67014 122.62608 DIRECTION COSINES OF ROTATION AXIS -0.77818 0.21332 -0.59070 DAVE SMITH -90.26013 58.14014 -31.62930
Product matrix = Rbasic * Rsecondary Matrix nr & determinant .. 3 1.000000 0.53352 -0.64166 -0.55103 0.20970 -0.53081 0.82114 -0.81938 -0.55365 -0.14864
CROWTHER ALPHA BETA GAMMA 123.86369 98.54844 -34.04647 SPHERICAL POLARS OMEGA PHI CHI 58.70922 168.95517 124.95725 DIRECTION COSINES OF ROTATION AXIS -0.83871 0.16371 0.51938 DAVE SMITH -100.26073 145.02281 50.25731
Product matrix = Rbasic * INV(Rsecondary) Matrix nr & determinant .. 4 1.000000 0.47773 0.87568 0.07043 0.87850 -0.47605 -0.04015 -0.00163 0.08105 -0.99671
CROWTHER ALPHA BETA GAMMA 150.31111 -175.35010 -91.15535 SPHERICAL POLARS OMEGA PHI CHI 88.85193 30.73316 175.95630 DIRECTION COSINES OF ROTATION AXIS 0.85939 0.51094 0.02004 DAVE SMITH -2.30700 -90.09373 118.61520
Enter next operator ...
Thank you and goodbye ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 4) 5 File with AMORE TF solutions ? (amore_tf.log) combi_p43_traing.log File for good solutions ? (amore_okay.log) File for poor solutions ? (amore_noway.log) Nr of lines read from file : ( 13826) Nr of SOLUTIONT lines read : ( 976) Nr with reasonable packing : ( 22) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? ( 1) 6 Step size (A) ? ( 5.000) 10 Nr of steps : ( 15 15 6) Step sizes : ( 6.667E-02 6.667E-02 1.667E-01) Positions to test : ( 1822500) #Tried 5000 #Okay 0 % 0.0 Max dist 0.00 #Tried 10000 #Okay 0 % 0.0 Max dist 9.33 ... #Tried 1815000 #Okay 193968 % 10.7 Max dist 38.90 #Tried 1820000 #Okay 193968 % 10.7 Max dist 38.90Positions tried : ( 1822500) No clashes for : ( 193968) % of cell okay : ( 10.643) Max distance : ( 38.897) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Fri Dec 18 19:42:22 1998
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